Difference between revisions of "ENST00000504263.1"

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Please input one-sentence summary here.
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''PCAT4'', 2091 bp long non-coding RNA, prostate cancer associated transcript.4,upregulated by NKX3.1, functions in the diagnosis or treatment of prostate cancer.
  
 
==Annotated Information==
 
==Annotated Information==
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===Transcriptomic Nomeclature===
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===Name===
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Please input transcriptomic nomeclature information here.
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''PCAT4'':prostate cancer associated transcript 4 (non-protein coding)(HGNC nomenclature)
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''GDEP'', "gene differentially expressed in prostate"<ref name="ref1" />
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''PCA4'', ''PCAN1'', "prostate cancer gene 1"<ref name="ref2" />
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===Characteristics===
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The major GDEP transcript is about 520 bp long and its transcript consists of two exons with one large intron (> 15 kb). The GDEP gene was mapped tochromosome 4q21.1.<ref name="ref1" />
  
 
===Function===
 
===Function===
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Please input function information here.
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The prostate specificity of GDEP expression indicates that GDEP may be useful in the diagnosis or treatment of prostate cancer<ref name="ref1" />.
  
 
===Regulation===
 
===Regulation===
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Please input regulation information here.
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NKX3.1 upregulated PCAN1 gene transcription in LNCaP prostate cancer cells<ref name="ref3" />
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===Diseases===
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* prostate cancer<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />
  
 
===Expression===
 
===Expression===
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Please input expression information here.
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A high level of expression of PCAN1 in human neural retina and retinoblastoma cells but little to no expression in the RPE, even for very early passage primary cell lines<ref name="ref2" />
  
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===Allelic Information and Variation===
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PCR reactions were performed using 2 µL of the resultant cDNA and the following primers
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Please input allelic information and variation information here.
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{|class='wikitable' style="text-align:center"
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|-
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| | PCAN1 372F
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| | 5'-GCGATGTGCTGTGAAATCTA<ref name="ref2" />
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|-
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| | PCAN1 771R
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| | 5'-CTTTCACATTCCCCGTGGT<ref name="ref2" />
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|-
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| |  Actin 3F
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| | 5'-GCTGTCAGAGTGGTTATGT<ref name="ref2" />
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|-
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| | Actin 3R
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| | 5'-ACATTGACGTACAGAGAGAG<ref name="ref2" />
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|}
  
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===Evolution===
 
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Please input evolution information here.
 
  
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You can also add sub-section(s) at will.
 
  
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
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Please input related labs here.
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* Laboratory of Molecular Biology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA.<ref name="ref1" />
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* Department of Marshfield Clinic Research Foundation, Marshfield, WI, USA.<ref name="ref2" />
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* Institute of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, 250012, China.<ref name="ref3" />
  
 
==References==
 
==References==
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Please input cited references here.
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<references>
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<ref name="ref1">Olsson P, Bera TK, Essand M, Kumar V, Duray P, Vincent J, et al. GDEP, a new gene differentially expressed in normal prostate and prostate cancer[J]. The Prostate. 2001,48(4):231-41.</ref>(1)
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<ref name="ref2">ross D, Reding DJ, Salzman SA, Zhang KQ, Catalona WJ, Burke J, et al. Expression and initial promoter characterization of PCAN1 in retinal tissue and prostate cell lines[J]. Medical oncology. 2004,21(2):145-53.</ref>(2)
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<ref name="ref3">Liu W, Zhang P, Chen W, Yu C, Cui F, Kong F, et al. Characterization of two functional NKX3.1 binding sites upstream of the PCAN1 gene that are involved in the positive regulation of PCAN1 gene transcription[J]. BMC molecular biology. 2008,9:45.</ref>(3)
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</references>
  
 
{{basic|
 
{{basic|
 
tID = ENST00000504263.1|
 
tID = ENST00000504263.1|
 
source = Gencode19|
 
source = Gencode19|
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same = lnc-PRDM8-1:1|
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same = lnc-PRDM8-1:1,''PCAT4'', ''GDEP'', ''PCA4'',  ''PCAN1''|
 
classification = intergenic|
 
classification = intergenic|
 
length = 2091 nt|
 
length = 2091 nt|
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sequence = <dnaseq>AAAGTGAGAGAGGGAGGCAGAAGAGGAAGTCAGAGCGATGTGCTGTGAAATCTACTACCGTTTGCTGGTTTTGAAAATGGAGAAAAAGAGTGAGGAACTGAGAAACATGGATGGCCTTGGGAACGTGGAAAAGGGTCACTGAAATGGGACGACATGAACTCAAGGAGGCTATTTATGACCATGTCATTTGCAACATGAAGAAAGCTTATCTGGAGTGAAAGTAAATGAGACCAACAGAGATGAGAGACCCGGAGAAATCCTGGTTACACTGCTTGAATCCTGTCAGTCCTATACTGGAGTCCTGTTAATACAAAATAATAGTAATAATCCCTCTGTTTCTTATGTTTATGCCAACTTCAACAAAAAGAAACTTGACTAAGAGACAATATAAGAATTTAATGTGTAATTAAGAAAGAACTCTCCACCACGGGGAATGTGAAAGGTATATGAGTCCCTTTTCACGATGCGATGTCATGTCTTTTAAATAAGCCATACTTTATGTTCAATAAAAAGAGAATAAGCAGGATTCGCAAGAGAACACAATCCCTTTTTAACTGCTGGGAAGATACTTTTAGTCATTAATGACTGGACGACAATTTGGGACACATATATGGATATTGGCCGGTTTGTGATGATGTGATTGGGCCTCTAAGTGACAACATTGTTCCCTGTATAGAGTGAGTGGCAAGTGCATTTATAAAATTGGCCATCATGGCTGTTAAATTTATGAGTCTAGAAGTGTGCCTCTCAAACAAGTATTTGAGAGGTTATCATGAAGAAAAACAAAATTAAAATTATTCTGCTGAGCTCTCAAAGGCAGAACTATTGAATCAAAATTATAGGAAGGAAGGTTCAAACCAACAATAAGAATGCCTCTCTTGCATTCCTCATCACTAGAAGTTTCTGATAAGATTTTTAGAAAAATTTAGACAGTATTCTTGAATTGAGCAGGGGGATAACACAGAGATAATTCAAATGTGGTTTGATGAACTTCTAAAATGGTTCCAACTATAAACTTCAATTATTCTAGCCTCCAAGACCTACACATAACTGTGCAATGTGCAAATTATTCAATAGTAACATAGAATTCTGAATAATTAGCATTTTCTCATGGTTTGATATTTGTATAAAGCAATCTTAGCAGTCTGAATAACTAGAATACTTCAAAGCAATATGTTTTATTGCTTTATATTTAAAGAAACCATGTCAGACATTTAAAATGAATGGCTGCTATCAGGAAAATGGATCTCAAGACACAAGAAATAAATCACAATGACTTCCTTATTTGTGGAAATTCTTCTTGTACTAGAAAGGAAAAGTAGAAGTATGGGAAAATGTCTTCCAGAAAATTACATTTTCCCAAAGTTTATTTTAAATTTTAATAATTTAATCAACCATCTGATTCTGATTTCAAGTGTCACAGAAGTTCATTTTATTATAAACAACAACAAAAAAACTTTGTAGTCTTGTAAACACTGGTGACAGAGAATAACACCACTAACCATGCTGAGCAGAAAACAGGAGCCAAGTAAGGGAAAAAGATTCTTTATGTCACTCATCAATTTAAAAGTGTTTTTCACCCCAGGACCATCCTGAAGCCAAAACTGGGGAAACATTTACTACTTTTACAAACAAAAATTTATATTCCATCCCTTGCATGATGTGTGTGTCTCCGACATTTGGTTTCTGTCTTAAGTGTCTAAAGAAAGGCCTTATTTAGAGCAAAATACATTTTTGTGGGCATTGATGTGAATTTCAGGTCTGGGTTATCAATGACCTAAATTGAGAAAATAGAGGGGCTGTGTGGACAAGGAGAGAGAAGAGAGCATACAGCTGCCCTATGCCGTTGCTCTGTTCACAGTAAGGATTGAGCCATTCTAATCCCCTTGGATTTTTTATCTACCAAAACAGCTTGGGCCCATCAGCAAATTGCAGTGGCATATGGTCCAGGTTTACGAGTAATCTGGCACATGATTAAGGCAAGGGGGATGTCATCTTTCAGCAAATACTGAAAATATTGTAGAAGAATTTGGTAGAGTTTTTAAATTCAAACTGATAAAATTGTAACTATTAAATACTTCCCCAAATCAA</dnaseq>|
 
sequence = <dnaseq>AAAGTGAGAGAGGGAGGCAGAAGAGGAAGTCAGAGCGATGTGCTGTGAAATCTACTACCGTTTGCTGGTTTTGAAAATGGAGAAAAAGAGTGAGGAACTGAGAAACATGGATGGCCTTGGGAACGTGGAAAAGGGTCACTGAAATGGGACGACATGAACTCAAGGAGGCTATTTATGACCATGTCATTTGCAACATGAAGAAAGCTTATCTGGAGTGAAAGTAAATGAGACCAACAGAGATGAGAGACCCGGAGAAATCCTGGTTACACTGCTTGAATCCTGTCAGTCCTATACTGGAGTCCTGTTAATACAAAATAATAGTAATAATCCCTCTGTTTCTTATGTTTATGCCAACTTCAACAAAAAGAAACTTGACTAAGAGACAATATAAGAATTTAATGTGTAATTAAGAAAGAACTCTCCACCACGGGGAATGTGAAAGGTATATGAGTCCCTTTTCACGATGCGATGTCATGTCTTTTAAATAAGCCATACTTTATGTTCAATAAAAAGAGAATAAGCAGGATTCGCAAGAGAACACAATCCCTTTTTAACTGCTGGGAAGATACTTTTAGTCATTAATGACTGGACGACAATTTGGGACACATATATGGATATTGGCCGGTTTGTGATGATGTGATTGGGCCTCTAAGTGACAACATTGTTCCCTGTATAGAGTGAGTGGCAAGTGCATTTATAAAATTGGCCATCATGGCTGTTAAATTTATGAGTCTAGAAGTGTGCCTCTCAAACAAGTATTTGAGAGGTTATCATGAAGAAAAACAAAATTAAAATTATTCTGCTGAGCTCTCAAAGGCAGAACTATTGAATCAAAATTATAGGAAGGAAGGTTCAAACCAACAATAAGAATGCCTCTCTTGCATTCCTCATCACTAGAAGTTTCTGATAAGATTTTTAGAAAAATTTAGACAGTATTCTTGAATTGAGCAGGGGGATAACACAGAGATAATTCAAATGTGGTTTGATGAACTTCTAAAATGGTTCCAACTATAAACTTCAATTATTCTAGCCTCCAAGACCTACACATAACTGTGCAATGTGCAAATTATTCAATAGTAACATAGAATTCTGAATAATTAGCATTTTCTCATGGTTTGATATTTGTATAAAGCAATCTTAGCAGTCTGAATAACTAGAATACTTCAAAGCAATATGTTTTATTGCTTTATATTTAAAGAAACCATGTCAGACATTTAAAATGAATGGCTGCTATCAGGAAAATGGATCTCAAGACACAAGAAATAAATCACAATGACTTCCTTATTTGTGGAAATTCTTCTTGTACTAGAAAGGAAAAGTAGAAGTATGGGAAAATGTCTTCCAGAAAATTACATTTTCCCAAAGTTTATTTTAAATTTTAATAATTTAATCAACCATCTGATTCTGATTTCAAGTGTCACAGAAGTTCATTTTATTATAAACAACAACAAAAAAACTTTGTAGTCTTGTAAACACTGGTGACAGAGAATAACACCACTAACCATGCTGAGCAGAAAACAGGAGCCAAGTAAGGGAAAAAGATTCTTTATGTCACTCATCAATTTAAAAGTGTTTTTCACCCCAGGACCATCCTGAAGCCAAAACTGGGGAAACATTTACTACTTTTACAAACAAAAATTTATATTCCATCCCTTGCATGATGTGTGTGTCTCCGACATTTGGTTTCTGTCTTAAGTGTCTAAAGAAAGGCCTTATTTAGAGCAAAATACATTTTTGTGGGCATTGATGTGAATTTCAGGTCTGGGTTATCAATGACCTAAATTGAGAAAATAGAGGGGCTGTGTGGACAAGGAGAGAGAAGAGAGCATACAGCTGCCCTATGCCGTTGCTCTGTTCACAGTAAGGATTGAGCCATTCTAATCCCCTTGGATTTTTTATCTACCAAAACAGCTTGGGCCCATCAGCAAATTGCAGTGGCATATGGTCCAGGTTTACGAGTAATCTGGCACATGATTAAGGCAAGGGGGATGTCATCTTTCAGCAAATACTGAAAATATTGTAGAAGAATTTGGTAGAGTTTTTAAATTCAAACTGATAAAATTGTAACTATTAAATACTTCCCCAAATCAA</dnaseq>|
 
}}
 
}}
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[[Category:Intergenic]]
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[[Category:Intergenic]][[Category:ENSG00000251321.1]][[Category:lnc-PRDM8-1]][[Category:Transcripts]][[Category:Transcripts]]

Latest revision as of 06:34, 25 June 2016

PCAT4, 2091 bp long non-coding RNA, prostate cancer associated transcript.4,upregulated by NKX3.1, functions in the diagnosis or treatment of prostate cancer.

Annotated Information

Name

PCAT4:prostate cancer associated transcript 4 (non-protein coding)(HGNC nomenclature)

GDEP, "gene differentially expressed in prostate"[1]

PCA4, PCAN1, "prostate cancer gene 1"[2]

Characteristics

The major GDEP transcript is about 520 bp long and its transcript consists of two exons with one large intron (> 15 kb). The GDEP gene was mapped tochromosome 4q21.1.[1]

Function

The prostate specificity of GDEP expression indicates that GDEP may be useful in the diagnosis or treatment of prostate cancer[1].

Regulation

NKX3.1 upregulated PCAN1 gene transcription in LNCaP prostate cancer cells[3]

Diseases

Expression

A high level of expression of PCAN1 in human neural retina and retinoblastoma cells but little to no expression in the RPE, even for very early passage primary cell lines[2]

PCR reactions were performed using 2 µL of the resultant cDNA and the following primers

PCAN1 372F 5'-GCGATGTGCTGTGAAATCTA[2]
PCAN1 771R 5'-CTTTCACATTCCCCGTGGT[2]
Actin 3F 5'-GCTGTCAGAGTGGTTATGT[2]
Actin 3R 5'-ACATTGACGTACAGAGAGAG[2]


Labs working on this lncRNA

  • Laboratory of Molecular Biology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA.[1]
  • Department of Marshfield Clinic Research Foundation, Marshfield, WI, USA.[2]
  • Institute of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, 250012, China.[3]

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Olsson P, Bera TK, Essand M, Kumar V, Duray P, Vincent J, et al. GDEP, a new gene differentially expressed in normal prostate and prostate cancer[J]. The Prostate. 2001,48(4):231-41.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 ross D, Reding DJ, Salzman SA, Zhang KQ, Catalona WJ, Burke J, et al. Expression and initial promoter characterization of PCAN1 in retinal tissue and prostate cell lines[J]. Medical oncology. 2004,21(2):145-53.
  3. ↑ 3.0 3.1 3.2 Liu W, Zhang P, Chen W, Yu C, Cui F, Kong F, et al. Characterization of two functional NKX3.1 binding sites upstream of the PCAN1 gene that are involved in the positive regulation of PCAN1 gene transcription[J]. BMC molecular biology. 2008,9:45.

Basic Information

Transcript ID

ENST00000504263.1

Source

Gencode19

Same with

lnc-PRDM8-1:1,PCAT4, GDEP, PCA4, PCAN1

Classification

intergenic

Length

2091 nt

Genomic location

chr4+:80748625..80784401

Exon number

2

Exons

80748625..80748757,80782444..80784401

Genome context

Sequence
000001 AAAGTGAGAG AGGGAGGCAG AAGAGGAAGT CAGAGCGATG TGCTGTGAAA TCTACTACCG TTTGCTGGTT TTGAAAATGG 000080
000081 AGAAAAAGAG TGAGGAACTG AGAAACATGG ATGGCCTTGG GAACGTGGAA AAGGGTCACT GAAATGGGAC GACATGAACT 000160
000161 CAAGGAGGCT ATTTATGACC ATGTCATTTG CAACATGAAG AAAGCTTATC TGGAGTGAAA GTAAATGAGA CCAACAGAGA 000240
000241 TGAGAGACCC GGAGAAATCC TGGTTACACT GCTTGAATCC TGTCAGTCCT ATACTGGAGT CCTGTTAATA CAAAATAATA 000320
000321 GTAATAATCC CTCTGTTTCT TATGTTTATG CCAACTTCAA CAAAAAGAAA CTTGACTAAG AGACAATATA AGAATTTAAT 000400
000401 GTGTAATTAA GAAAGAACTC TCCACCACGG GGAATGTGAA AGGTATATGA GTCCCTTTTC ACGATGCGAT GTCATGTCTT 000480
000481 TTAAATAAGC CATACTTTAT GTTCAATAAA AAGAGAATAA GCAGGATTCG CAAGAGAACA CAATCCCTTT TTAACTGCTG 000560
000561 GGAAGATACT TTTAGTCATT AATGACTGGA CGACAATTTG GGACACATAT ATGGATATTG GCCGGTTTGT GATGATGTGA 000640
000641 TTGGGCCTCT AAGTGACAAC ATTGTTCCCT GTATAGAGTG AGTGGCAAGT GCATTTATAA AATTGGCCAT CATGGCTGTT 000720
000721 AAATTTATGA GTCTAGAAGT GTGCCTCTCA AACAAGTATT TGAGAGGTTA TCATGAAGAA AAACAAAATT AAAATTATTC 000800
000801 TGCTGAGCTC TCAAAGGCAG AACTATTGAA TCAAAATTAT AGGAAGGAAG GTTCAAACCA ACAATAAGAA TGCCTCTCTT 000880
000881 GCATTCCTCA TCACTAGAAG TTTCTGATAA GATTTTTAGA AAAATTTAGA CAGTATTCTT GAATTGAGCA GGGGGATAAC 000960
000961 ACAGAGATAA TTCAAATGTG GTTTGATGAA CTTCTAAAAT GGTTCCAACT ATAAACTTCA ATTATTCTAG CCTCCAAGAC 001040
001041 CTACACATAA CTGTGCAATG TGCAAATTAT TCAATAGTAA CATAGAATTC TGAATAATTA GCATTTTCTC ATGGTTTGAT 001120
001121 ATTTGTATAA AGCAATCTTA GCAGTCTGAA TAACTAGAAT ACTTCAAAGC AATATGTTTT ATTGCTTTAT ATTTAAAGAA 001200
001201 ACCATGTCAG ACATTTAAAA TGAATGGCTG CTATCAGGAA AATGGATCTC AAGACACAAG AAATAAATCA CAATGACTTC 001280
001281 CTTATTTGTG GAAATTCTTC TTGTACTAGA AAGGAAAAGT AGAAGTATGG GAAAATGTCT TCCAGAAAAT TACATTTTCC 001360
001361 CAAAGTTTAT TTTAAATTTT AATAATTTAA T