Difference between revisions of "NONHSAT016928"

Latest revision as of 05:46, 26 August 2015

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Annotated Information

Name

CAR10: Chromatin Associated RNA 10

Characteristics

Positioned between 3' ends of of FANK1 (fibronectin) and ADAM12 (ADAM metallopeptidase domain 12) genes, with an overlap of a few hundred base pairs with ADAM12.

Function

Positively regulates gene expression of FANK1 and ADAM12 neighboring genes through modulating the chromatin structure in cis, as siRNA knock-down of the Intergenic10 ncRNA results in reduced expression of both FANK1 and ADAM12 mRNAs, with a significant decrease in the level of active chromatin mark H3K4me2 on FANK1 and ADAM12 promoters.. Knock-down of the ncRNA had no effect on the expression of two tested distal genes, UROS and DOCK1.. Note: Despite its overlap with the 3' end of ADAM12, Intergenic 10 is not simply an Adam12 3'UTR, as siRNA knockdown of Adam12 failed to decrease FANK1 expression unlike knockdown of CAR Intergenic 10.

Expression

CAR Intergenic 10, ADAM12 and FANK1 are co-expressed in different tissues, including placenta, brain and a human skin fibroblast (HF) cell line. . CAR Intergenic 10 was most highly expressed in HF cells and very lowly expressed in brain, with placenta in-between.

Conservation

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Misc

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Transcriptomic Nomeclature

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Regulation

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Allelic Information and Variation

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Evolution

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Labs working on this lncRNA

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References

Annotation originally sourced from lncRNAdb.

Basic Information

Transcript ID	NONHSAT016928
Source	NONCODE4.0
Same with	,
Classification	sense
Length	2375 nt
Genomic location	chr10-:127700956..127703336
Exon number	1
Exons	127700956..127703336
Genome context
Sequence	000001 AATGTGACTA GACACAAAGT AGCCCAGAGG CTACTTTTCT TCCTACAGCT TATTATAGTT GTAGGTTCTA TGACCTCACT 000080 000081 TCATGGGTTC CAGGCAATTC CGCTGAAAGG TTTGTCTCCT GAAATTTTTT AAGTTTGTTT TCCTGACACA TGTAATCAGA 000160 000161 TGTGTAGCAA CCGAGGGAAA CGAAGCCTAA CATTCTCCAT TGTGGAAATA CACACAGGAG GTTACACTTC ACAGCGTGGA 000240 000241 TTTTTCCAGC TTACACATGT GGGATGACAT CACAGAAACC ACAAAAGCAG CAAATTAAAC TGTAGGAGAG TCAATACTCC 000320 000321 TGACGAGTCT CGGGGGGGGC ATTTTTATGC CTTCTTAACT TTATGAGAAT TCTCAGGCTG AACTATAGGC CATTGTTCCC 000400 000401 AGGCAAATCA ATACAGCAAT GCATCCTCAA AAAAAAAAAA AAAAAAAAAC GGCTAAAACT GTGTCAAAAT GTTCTTAAGG 000480 000481 AGCCTATGGT CTCCACGGTG CTAAAAAGAG CCTGGTGCTG GGCCGACTGG CAGGGCTGAG CATCCTCCTG CCCCCTCGCC 000560 000561 ACTGATGTTT ACTAAGCACT CTGAGCCAAT GAGACCCCCA GCAGCAGAAA GGGCACAAGG TGGCGCCAGG GCAGCAGGGC 000640 000641 CAGATCTTTC TCATGCACCT CGACCTCTTG CAGACTTTCT TCGTGAGATG TACTACTCAT TTCAAAACTG CTTTGCAGGG 000720 000721 CTCCCCTATG TATTCGGGGG GCCCACGGCA CACTCAGGCT GGAGATCCTT CCTCACTGCG CTCAAGATGG CCTCAGCCAG 000800 000801 ACACCAGTTA CCCAGCTGAA AGTCACAATC CCTCCCAGAA GTCTCCCAAC ACTAGTGCTG ACCAGAGGTG GGGCTCTCAG 000880 000881 GCTAGGAGTT TCACACACAA TGACAGGCTG CTGGGGGACA TTGCAGGACC CCTTTTCCTC TCCTCTCCAT GCTAGAAGCC 000960 000961 AGCCCTAGGC AGCTGCAGTT ACTCCCTGTG ACTCAGCAGC AGGCTGATTC AACACAGCTG CCCACACAAA GCCAGTGGCT 001040 001041 AATACATCTG TTTACCTTTC CCTATCACCC AGACACAAGC CCCTTTCCCA GGTCAAACCA CAGGCCGATG CATCTCCAGT 001120 001121 TTGACAGTCA AATCACTACT TCCATTGCTA CTTTAGATCA GCCAAAGTGG TGACTGCTGC AGTGTGTGGC TATCCCTACA 001200 001201 AGGCCCACCC AAGGGATGCC CAAAGCCCAA CCTTCTCCAG GGCTGCAGCC CAGAGCAACC CCACCAGCCT AAGTCCAGCA 001280 001281 GAGGACCTCC CACCCAATGT CTTGTTCTAA TTAGAAGGGG AAGTTAGCCA CAGAAAATCA ACTTATCTAT AATTACAAAA 001360 001361 TTCTCTTGAC TCACCTTAAA GTTCCTATTG ACATCTACTG CTTTTAAACC TATTTGAAAA CTCTGATACT AAAACAAATG 001440 001441 ACACTCTAAG AAAGTTTGGG AGCCCCATGC TGAGAACCAT TTCTGTGCAG TGAGGATGTT TCCAGAAGCT ACTTACCTAC 001520 001521 ATGTGAATGT GCCATTTTCT TTCCTTTTGT AGAGAAAATC CCCTTTACTT TTTGGAACAG TAATGGCAGC

@@ Line 2: / Line 2: @@
 ==Annotated Information==
+===Name===
+CAR10: Chromatin Associated RNA 10
+===Characteristics===
+Positioned between 3' ends of of FANK1 (fibronectin) and ADAM12 (ADAM metallopeptidase domain 12) genes, with an overlap of a few hundred base pairs with ADAM12.
+===Function===
+Positively regulates gene expression of FANK1 and ADAM12 neighboring genes through modulating the chromatin structure in cis, as siRNA knock-down of the Intergenic10 ncRNA results in reduced expression of both FANK1 and ADAM12 mRNAs, with a significant decrease in the level of active chromatin mark H3K4me2 on FANK1 and ADAM12 promoters.. Knock-down of the ncRNA had no effect on the expression of two tested distal genes, UROS and DOCK1.. Note: Despite its overlap with the 3' end of ADAM12, Intergenic 10 is not simply an Adam12 3'UTR, as siRNA knockdown of Adam12 failed to decrease FANK1 expression unlike knockdown of CAR Intergenic 10.
+===Expression===
+CAR Intergenic 10, ADAM12 and FANK1 are co-expressed in different tissues, including placenta, brain and a human skin fibroblast (HF) cell line. . CAR Intergenic 10 was most highly expressed in HF cells and very lowly expressed in brain, with placenta in-between.
+===Conservation===
+Please input conservation information here.
+===Misc===
+Please input misc information here.
 ===Transcriptomic Nomeclature===
 Please input transcriptomic nomeclature information here.
-===Function===
-Please input function information here.
 ===Regulation===
 Please input regulation information here.
-===Expression===
-Please input expression information here.
 ===Allelic Information and Variation===
@@ Line 26: / Line 38: @@
 ==References==
-Please input cited references here.
+[http://www.lncrnadb.org/carintergenic10/ Annotation originally sourced from lncRNAdb.]
 {{basic|
@@ Line 42: / Line 54: @@
 sequence = <dnaseq>AATGTGACTAGACACAAAGTAGCCCAGAGGCTACTTTTCTTCCTACAGCTTATTATAGTTGTAGGTTCTATGACCTCACTTCATGGGTTCCAGGCAATTCCGCTGAAAGGTTTGTCTCCTGAAATTTTTTAAGTTTGTTTTCCTGACACATGTAATCAGATGTGTAGCAACCGAGGGAAACGAAGCCTAACATTCTCCATTGTGGAAATACACACAGGAGGTTACACTTCACAGCGTGGATTTTTCCAGCTTACACATGTGGGATGACATCACAGAAACCACAAAAGCAGCAAATTAAACTGTAGGAGAGTCAATACTCCTGACGAGTCTCGGGGGGGGCATTTTTATGCCTTCTTAACTTTATGAGAATTCTCAGGCTGAACTATAGGCCATTGTTCCCAGGCAAATCAATACAGCAATGCATCCTCAAAAAAAAAAAAAAAAAAAAACGGCTAAAACTGTGTCAAAATGTTCTTAAGGAGCCTATGGTCTCCACGGTGCTAAAAAGAGCCTGGTGCTGGGCCGACTGGCAGGGCTGAGCATCCTCCTGCCCCCTCGCCACTGATGTTTACTAAGCACTCTGAGCCAATGAGACCCCCAGCAGCAGAAAGGGCACAAGGTGGCGCCAGGGCAGCAGGGCCAGATCTTTCTCATGCACCTCGACCTCTTGCAGACTTTCTTCGTGAGATGTACTACTCATTTCAAAACTGCTTTGCAGGGCTCCCCTATGTATTCGGGGGGCCCACGGCACACTCAGGCTGGAGATCCTTCCTCACTGCGCTCAAGATGGCCTCAGCCAGACACCAGTTACCCAGCTGAAAGTCACAATCCCTCCCAGAAGTCTCCCAACACTAGTGCTGACCAGAGGTGGGGCTCTCAGGCTAGGAGTTTCACACACAATGACAGGCTGCTGGGGGACATTGCAGGACCCCTTTTCCTCTCCTCTCCATGCTAGAAGCCAGCCCTAGGCAGCTGCAGTTACTCCCTGTGACTCAGCAGCAGGCTGATTCAACACAGCTGCCCACACAAAGCCAGTGGCTAATACATCTGTTTACCTTTCCCTATCACCCAGACACAAGCCCCTTTCCCAGGTCAAACCACAGGCCGATGCATCTCCAGTTTGACAGTCAAATCACTACTTCCATTGCTACTTTAGATCAGCCAAAGTGGTGACTGCTGCAGTGTGTGGCTATCCCTACAAGGCCCACCCAAGGGATGCCCAAAGCCCAACCTTCTCCAGGGCTGCAGCCCAGAGCAACCCCACCAGCCTAAGTCCAGCAGAGGACCTCCCACCCAATGTCTTGTTCTAATTAGAAGGGGAAGTTAGCCACAGAAAATCAACTTATCTATAATTACAAAATTCTCTTGACTCACCTTAAAGTTCCTATTGACATCTACTGCTTTTAAACCTATTTGAAAACTCTGATACTAAAACAAATGACACTCTAAGAAAGTTTGGGAGCCCCATGCTGAGAACCATTTCTGTGCAGTGAGGATGTTTCCAGAAGCTACTTACCTACATGTGAATGTGCCATTTTCTTTCCTTTTGTAGAGAAAATCCCCTTTACTTTTTGGAACAGTAATGGCAGCTTCTAGTACAGCCATTACAGTTTCATATGAGAAAAATTAAGAATAACTATAAAATTGTTAAAATATCCAATAATGGATAATGATGGCCAGAAGATTTAACATACAAAGTAATTCTCAATGTAAAGCTATTCAGCTCTTCCAGGTTGAATGCCCTGTAACCCACCCTGACCTTCCACATCATCTTCAAAAAGCAGTTTCTCTGTTCCCCATGATTCTCCTATAAGGTAACTCTTTAGTCCTCCATTTAGCACATTTTAAATCCTCCAAAGAATAAGTATCATGTGATTATTTTAGCTTTACAAAAAAAAAGTTGAATGGCGTTTTATTTTCATGGCCTATAAGCAGGTACCTTAGTAGGGCAGATATAGGAAAAACAAATTAGAGCAAAACAAATCCTCTACAAATCCAAGGCAGGAAAAGTGGTGGCAGAGTGACTCATTCTCCTGTCCCTCCCATCAGGTCAAATCAGGAGGCTGCAGTGAATGCCTGTTCTTTGAATGTGTAGCAGTTGTTCCTGTAACTCTTTAAAACTTGGCTATAGGCTGTTTAGCACAGTACAGATTAAAGATACAGTTACGTAAACAGCAAAGTAATTTTATAGTGCTTCATCCATTTATCATGCTTTGGTTTGCTAATTTTTTCACATACCTTTTTCTATCACAGTCTGTTGCTTTTGTACACATTTCTCATATTGGGGTTCGACAGGTAAACACAAACTGCTATTTCAGTAGAAAAAGTTATTGTTATGAATATTAAACCCAATAAATTGTATAAAGGTAAATATC</dnaseq>|
 }}
-[[Category:Sense]]
+[[Category:Sense]][[Category:NONHSAG007141]][[Category:Transcripts]][[Category:Transcripts]]
-{{lncrnadb|
-tID = NONHSAT016928|
-ltID = CAR Intergenic 10|
-ann = <tab class=wikitable sep=tab head=top>
-Section	Description
-ID	CAR Intergenic 10
-Name	CAR10: Chromatin Associated RNA 10
-Characteristics	Positioned between 3' ends of of FANK1 (fibronectin) and ADAM12 (ADAM metallopeptidase domain 12) genes, with an overlap of a few hundred base pairs with ADAM12.
-Expression	CAR Intergenic 10, ADAM12 and FANK1 are co-expressed in different tissues, including placenta, brain and a human skin fibroblast (HF) cell line. . CAR Intergenic 10 was most highly expressed in HF cells and very lowly expressed in brain, with placenta in-between.
-Function	Positively regulates gene expression of FANK1 and ADAM12 neighboring genes through modulating the chromatin structure in cis, as siRNA knock-down of the Intergenic10 ncRNA results in reduced expression of both FANK1 and ADAM12 mRNAs, with a significant decrease in the level of active chromatin mark H3K4me2 on FANK1 and ADAM12 promoters.. Knock-down of the ncRNA had no effect on the expression of two tested distal genes, UROS and DOCK1.. Note: Despite its overlap with the 3' end of ADAM12, Intergenic 10 is not simply an Adam12 3'UTR, as siRNA knockdown of Adam12 failed to decrease FANK1 expression unlike knockdown of CAR Intergenic 10.
-</tab>|
-}}