Difference between revisions of "NONHSAT059436"

Latest revision as of 08:42, 28 June 2016

Please input one-sentence summary here.

Annotated Information

Name

LINC-ROR

Characteristics

2.6kb, four exons. Most of the sequence is composed of LINE, SINE and LTR elements.

Function

Functions to promote reprogramming of differentiated cells to iPSCs. - Knockdown decreased the number of iPSC colonies formed without affecting cell number. While over-expression increased the number of iPSC colonies formed. Functions in maintenance of ESCs and iPSCs. - Knockdown lead to modest increase in apoptosis and activation of p53 pathways.

Expression

LincRNA enriched in ESC (embryonic stem cells) and iPSCS (induced pluripotent stem cells) compared to the fibroblast and CD34 cells the iPSCs were derived from. Also more highly expressed in iPSCs than ESCs. Locus is a binding site for pluripotency transcription factors Oct4, Sox2 and Nanog. Knockdown of Oct4 or differentiation of stem cells caused down-regulation of lincRNA-RoR expression. Suggesting expression is controlled by these transcription factors.

Conservation

No syntenic correlate expressed in mouse ESCs. Some exons appear to be transcribed from human specific repeat sequences. While others appear limited to certain primates.

Misc

Please input misc information here.

Transcriptomic Nomeclature

Please input transcriptomic nomeclature information here.

Regulation

Please input regulation information here.

Allelic Information and Variation

Please input allelic information and variation information here.

Evolution

Please input evolution information here.

You can also add sub-section(s) at will.

Labs working on this lncRNA

Please input related labs here.

References

Annotation originally sourced from lncRNAdb.

Basic Information

Transcript ID	NONHSAT059436
Source	NONCODE4.0
Same with	,
Classification	intergenic
Length	2591 nt
Genomic location	chr18-:54721802..54739350
Exon number	4
Exons	54721802..54723481,54724731..54725231,54737041..54737234,54739135..54739350
Genome context
Sequence	000001 GGTGAAATAA ACAGCCATGT TGCTCACACA AAGCCTGTTT GGTGGTCTCT TCACACGGAC GCTCATGAAA TTTGGTGATG 000080 000081 TGACTCGGAT AGGGGGACCT CCCTTGGGAG ATCAGTACCC TGTCCTCCTG CTCTTTGCTC CGTGAGAAAG ATCCACCTAC 000160 000161 AACCTCAGGT CCTTAGACCA ACCAGCCCAA GAAACATCTC ACCAATTTCA AATCCAGACC CCACTGGAAA TCGGACTGTC 000240 000241 CAACTCACCT GACAGCCACT CCCACAGCCG CTGGAACTCT GGCCCAAGGC TCTCTGACTC CTTCCCAGAT CTTCTTGGCT 000320 000321 TAGCGGCTGA AGACTGACGC TGCCCGATCG CCTCGGAAGC CCCCTAGACC ATCACGGACG CCGAGCTTCG GGTAACTCTC 000400 000401 ACAGTGGAAG AAACACAACT ACAGATTTCT ACCTGGTGCA TGGCCATCGC TCATGAAGAC TACAACTTCC AGCTTCCTTT 000480 000481 GAAGAAAAAG AGGACTTGAT GGCATTGTCG CTAAGTAAGA AATAATGTGT GTGACTTCAG GGTTGCCCCC TTAAAGGGAG 000560 000561 GGGACATTTT CCATCCTGCT GTTCAGAGTA TGGATGTGAT GAGAGACATC TTGGATGATG CAGAGGAGGT GAACACCCCA 000640 000641 GGACAATGAA ACCACAGGAG AGAAAGAGCC TGCGCTGGCC CATCTAGCAC AGCCACTGGA CACAGGGACC ACCTGCCTCT 000720 000721 GCACTCTTAT GGAAGGAGGA AATCTAACTT TCCCAGTTTA AGGCACTGTT ACTTTGGGCT CCTGTTACAT AACTGTGGCA 000800 000801 GAATGAAGGT TCAACATGGA AACTGGCAAT GTTGAAGAAA CATAAAGTTC ATTGCTTGAA TATCTGAAGT TGTGGACTCA 000880 000881 ATCTCATACC TGCTCCACTT ATGAGTTATA GTTCTTCCAG GTCTCAGGAA TGGGATCAGC AGGTCTCAGG GTTGTACTCT 000960 000961 CCTGGATCTC TCACCAGCCA CCTCAAACCA GCTGCCATAG CCTGTCCACT TCCACTCCAA TCTTCTCTTC CTTCATCACC 001040 001041 TCCCTTGCAC ACCCTGATAA CCTCGAAAGA GAACTCTTCC CAAGGCTCTG TTCCAAACAC ATCGCCACTC TGCTTAGAAC 001120 001121 CTTCAATGAC TCCTCATGGC CTAGGAGGTT TCTCTCCCAT CTGGATCCAG CTGACGTTCC CAGCACCTTC TCCTGACTCC 001200 001201 TGTCTTTTCT TGAACCAGTT CTGCCCAACA AGGAGGAAAG GGCTGACAGA GTGAAAGTCC CAGGGCATGT GGGAATGTGA 001280 001281 CTCTTTTCAC TTTAAATTCT ATGACTGGAA AGTTTTGGGC AGAGTTGGAC ATGTGCACTT AGCTTCCAGA AGACAGAATC 001360 001361 CTTTTAAAAG AGTCAGAGAA AACACTGGCT TCCTGCCATG ACATGAGATA CAGACAGGAG AGTTGGGAAG CTTTTTAAAG 001440 001441 ATGGCACTAT GACTACAATC ACAGAAACTC TCCATGAGGA AGTAAAAGAA AGCACCTGCA ACACTCCAGC TATGCAGACC 001520 001521 ACTCTGTAAT GGGCTCAGAT CTGGACAGGT GTGTGGAAAG GTGGGTCAAC AGGTCAGGCG TCACAGAC

@@ Line 2: / Line 2: @@
 ==Annotated Information==
+===Name===
+LINC-ROR
+===Characteristics===
+.6kb, four exons. Most of the sequence is composed of LINE, SINE and LTR elements.
+===Function===
+Functions to promote reprogramming of differentiated cells to iPSCs. - Knockdown decreased the number of iPSC colonies formed without affecting cell number. While over-expression increased the number of iPSC colonies formed. Functions in maintenance of ESCs and iPSCs. - Knockdown lead to modest increase in apoptosis and activation of p53 pathways.
+===Expression===
+LincRNA enriched in ESC (embryonic stem cells) and iPSCS (induced pluripotent stem cells) compared to the fibroblast and CD34 cells the iPSCs were derived from. Also more highly expressed in iPSCs than ESCs. Locus is a binding site for pluripotency transcription factors Oct4, Sox2 and Nanog. Knockdown of Oct4 or differentiation of stem cells caused down-regulation of lincRNA-RoR expression. Suggesting expression is controlled by these transcription factors.
+===Conservation===
+No syntenic correlate expressed in mouse ESCs. Some exons appear to be transcribed from human specific repeat sequences. While others appear limited to certain primates.
+===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/lincRNA-RoR/ Annotation originally sourced from lncRNAdb.]
 {{basic|
@@ Line 42: / Line 54: @@
 sequence = <dnaseq>GGTGAAATAAACAGCCATGTTGCTCACACAAAGCCTGTTTGGTGGTCTCTTCACACGGACGCTCATGAAATTTGGTGATGTGACTCGGATAGGGGGACCTCCCTTGGGAGATCAGTACCCTGTCCTCCTGCTCTTTGCTCCGTGAGAAAGATCCACCTACAACCTCAGGTCCTTAGACCAACCAGCCCAAGAAACATCTCACCAATTTCAAATCCAGACCCCACTGGAAATCGGACTGTCCAACTCACCTGACAGCCACTCCCACAGCCGCTGGAACTCTGGCCCAAGGCTCTCTGACTCCTTCCCAGATCTTCTTGGCTTAGCGGCTGAAGACTGACGCTGCCCGATCGCCTCGGAAGCCCCCTAGACCATCACGGACGCCGAGCTTCGGGTAACTCTCACAGTGGAAGAAACACAACTACAGATTTCTACCTGGTGCATGGCCATCGCTCATGAAGACTACAACTTCCAGCTTCCTTTGAAGAAAAAGAGGACTTGATGGCATTGTCGCTAAGTAAGAAATAATGTGTGTGACTTCAGGGTTGCCCCCTTAAAGGGAGGGGACATTTTCCATCCTGCTGTTCAGAGTATGGATGTGATGAGAGACATCTTGGATGATGCAGAGGAGGTGAACACCCCAGGACAATGAAACCACAGGAGAGAAAGAGCCTGCGCTGGCCCATCTAGCACAGCCACTGGACACAGGGACCACCTGCCTCTGCACTCTTATGGAAGGAGGAAATCTAACTTTCCCAGTTTAAGGCACTGTTACTTTGGGCTCCTGTTACATAACTGTGGCAGAATGAAGGTTCAACATGGAAACTGGCAATGTTGAAGAAACATAAAGTTCATTGCTTGAATATCTGAAGTTGTGGACTCAATCTCATACCTGCTCCACTTATGAGTTATAGTTCTTCCAGGTCTCAGGAATGGGATCAGCAGGTCTCAGGGTTGTACTCTCCTGGATCTCTCACCAGCCACCTCAAACCAGCTGCCATAGCCTGTCCACTTCCACTCCAATCTTCTCTTCCTTCATCACCTCCCTTGCACACCCTGATAACCTCGAAAGAGAACTCTTCCCAAGGCTCTGTTCCAAACACATCGCCACTCTGCTTAGAACCTTCAATGACTCCTCATGGCCTAGGAGGTTTCTCTCCCATCTGGATCCAGCTGACGTTCCCAGCACCTTCTCCTGACTCCTGTCTTTTCTTGAACCAGTTCTGCCCAACAAGGAGGAAAGGGCTGACAGAGTGAAAGTCCCAGGGCATGTGGGAATGTGACTCTTTTCACTTTAAATTCTATGACTGGAAAGTTTTGGGCAGAGTTGGACATGTGCACTTAGCTTCCAGAAGACAGAATCCTTTTAAAAGAGTCAGAGAAAACACTGGCTTCCTGCCATGACATGAGATACAGACAGGAGAGTTGGGAAGCTTTTTAAAGATGGCACTATGACTACAATCACAGAAACTCTCCATGAGGAAGTAAAAGAAAGCACCTGCAACACTCCAGCTATGCAGACCACTCTGTAATGGGCTCAGATCTGGACAGGTGTGTGGAAAGGTGGGTCAACAGGTCAGGCGTCACAGACTTGGAACATTCATGGTGGAAAAGAAAAAGCCCCAAAGAAGAGACTTCAGGATAAATGAGAAAATACTCAAGACAGCAAAAGTCTCTTTTAGAAATGTTGGAGAAAGAACACTTAATGTCAGGAGTTACTGTTGATTGATGGCCTTACTGTGTAGCAGGTGAGAAACCCATTGTTCAGTTCCCTAAAGTCACCCTATTCTCCCAATCATCCTATGGAGGGGGAACCATGATGGTTATCCCCATCTTATAAATAAAGCAACAGAGGCTTAGAAGGACGAACTCTTTTTCTCAAGGTTACCCAGATCATTTTGCAGAAGTCCCTAGATTTGAATCATGCTCTTGCTTTGAGGTTAAAGACACAGGGGAAGTCGAACTCCTTATCTCCTATATCCTGAATAGGGAAAACCAAACATTGTCAAGAGGAGAGGAAGCCTGAGAGTTGGCATGAATCAGAGTGCTGGGCAGTCTGGAGTCTTCCCCACTGAGTTGATGATGGAACAGTAGAGTGGGGCCTGAGCCCCGTTAGGGCATGAGCTGCTGAATGATTCATGTGAACACCATGCACATGGGAGTGAGGTTTTGAGCAGTGTGCCACAGGAGCCTACCCTCAGGCCCCACCATAAAATGTAGGGCCAGTCCTACATTTTATCAATGACTTGCGTGAACACAGAAAATGTGGATACAACCAAAAGGTAACAATCCAATTAAAAAATGGACAAAAAACTTGAATAAACATTTCTCAAAAGAAGATATACAAATGATCAAAAAGCATATGAAAAAATGCTCAACATCGCTAATTGTAAGAGAAATGCAAATCAAAACTATAATGAGATACCACCTTATATTGATTAGGAAGACTGCTATAAAAATAGTAAACAAACAAACAAACAAAGTAAGTCTTGGGGAGGATGCAGAGAAATTAAAATTTTTGTGCACTGTTAGTGGGAATGTAAAATGGTGCAGCTGTTACGGGAAACGGTATGACAGTTCCTCAAAAAATAAAA</dnaseq>|
 }}
-[[Category:Intergenic]]
+[[Category:Intergenic]][[Category:NONHSAG023930]][[Category:Transcripts]]
-{{lncrnadb|
-tID = NONHSAT059436|
-ltID = lincRNA-RoR|
-ann = <tab class=wikitable sep=tab head=top>
-Section	Description
-ID	lincRNA-RoR
-Characteristics	2.6kb, four exons. Most of the sequence is composed of LINE, SINE and LTR elements.
-Expression	LincRNA enriched in ESC (embryonic stem cells) and iPSCS (induced pluripotent stem cells) compared to the fibroblast and CD34 cells the iPSCs were derived from. Also more highly expressed in iPSCs than ESCs. Locus is a binding site for pluripotency transcription factors Oct4, Sox2 and Nanog. Knockdown of Oct4 or differentiation of stem cells caused down-regulation of lincRNA-RoR expression. Suggesting expression is controlled by these transcription factors.
-Function	Functions to promote reprogramming of differentiated cells to iPSCs. - Knockdown decreased the number of iPSC colonies formed without affecting cell number. While over-expression increased the number of iPSC colonies formed. Functions in maintenance of ESCs and iPSCs. - Knockdown lead to modest increase in apoptosis and activation of p53 pathways.
-Conservation	No syntenic correlate expressed in mouse ESCs. Some exons appear to be transcribed from human specific repeat sequences. While others appear limited to certain primates.
-</tab>|
-}}