HsaINT0037945 @ hg19
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:2186]
Coordinates
chr1:103491077-103491888:-
Coord C1 exon
chr1:103491772-103491888
Coord A exon
chr1:103491170-103491771
Coord C2 exon
chr1:103491077-103491169
Length
602 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
TCTTCTGAATTTACCATTAGGCA
3' ss Score
6.09
Exon sequences
Seq C1 exon
TATGCACCAGAGGATATAATCGAATATGACTATGAGTATGGGGAAGCAGAGTATAAAGAGGCTGAAAGTGTAACAGAGGGACCCACTGTAACTGAGGAGACAATAGCACAGACGGAG
Seq A exon
GTAAAAACAAAGCAGTGCCTGTGTATGTGGTGTCCTGCTGTTCGTCATCCTGTGGTTCCTTATGTTGACTGTTCCTCAAACTTACCATAAACCTTTCATTCATCTTATTTCTCTGAACCAATAACTGTGATTTTTATTTGACAGTAGCCGTTTTGAAGAATGATGTCCATTTCACTTTTGCTTAGCCTTCCTTTCATCTGTGCTCTATATTTCCCTCCTCGTTTATTTATGTTTTCCATTCCATCTTTCACCACATTTTACAGAAAAAGAAATCCAATTTCAAAAAGAAGATGAGGACAGTGGCTACTAAATCAAAGGAAAAATCCAAAAAGTTTACACCCCCCAAATCTGAAAAATTTTCATCCAAGAAGAAGAAAAGTTATCAAGCATCAGCAAAAGCCAAACTAGGGGTAAAGGTAGCGAAGAAAAAGCAATCAAGATCTATCCTAGATAAGCTGGAAGATCTCTGATCATGAATCATAGTCTTAACCCAACTAGATAAATACTCACTTGGCTAATACTATAACCCAATTAAATCATGATTTCCATACATTTGGGATCACCTTACATGTTTACTAATTCTCTTCTGAATTTACCATTAG
Seq C2 exon
GCAAACATCGTTGATGATTTTCAAGAATACAACTATGGAACAATGGAAAGTTACCAGACAGAAGCTCCTAGGCATGTTTCTGGGACAAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718-COL11A1:NM_001854:6
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.885 A=NA C2=0.754
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCACCAGAGGATATAATCGAAT
R:
TCATTTGTCCCAGAAACATGCCT
Band lengths:
207-809
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)