HsaINT0037900 @ hg19
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:2186]
Coordinates
chr1:103453189-103455127:-
Coord C1 exon
chr1:103455074-103455127
Coord A exon
chr1:103453297-103455073
Coord C2 exon
chr1:103453189-103453296
Length
1777 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
GTTGTTATTCTGTGCCTCAGGGA
3' ss Score
6.94
Exon sequences
Seq C1 exon
GGTGAAGATGGTTTTCCAGGATTCAAAGGTGACATGGGTCTAAAAGGTGACAGA
Seq A exon
GTAAGTATAGAGAAAATGTACACCAGTACACAAAATTTAATATATATATATATTTTTTCCTTTGCTTATCTTTAAATATAGTAAGCATATGATAAATAAAATGTTTGTACTACCTAAGTCTTTACTCATTTAAGTTTTTATACAAAGATTTAAGGATTTTAATTTTTGTGGAGATAGTGTAGTATCAATTGTCTTTTAGATGTTATATTTCCATAGGTTCCATAATAAACATGAGCATGCACGCGTGCACACACACACACACACATGCACACACACGTGTTAGTATTTATACACAGGACATTAGAAAGTTAGATCAAATTACTAGAAGTAATTTGATAAGTTTGCTCTAAATTTTGTTCATATATAATGAGCTATGCTGCCTGGAAAGTATACGTCTGTAACTTTCATGAATTTTCATTATATGGTGGTGTTCAATTTTTGAATGTAAAAATAGTAGTTTTTTCTAGTAATACATTATAGAAAACAAACAGAAATATTAGTTATCTAAAGCAAATTAAATGCTTTATTGGGAAGATTTATTTTTAAGTAATATACTAGTACCTAATACATCTGAATAAAGAAGCATTCTATAGAAAATATTTCTTTTCCTAAAATTCAAATGAAGTCTGCATGCAGGATTGGGGGCAATAACATCCATATACAAGTTCTTAAACGTTAAAGATAAAAGCCACGTACAAAAGAGAGACATTTTTCTTGTGTTCCAAACAGTAATTTCCAAAGCTGCTGAACAATCTTTATTATTATTTTTCCCTCTCTCTATAACACAGGTGCATTAAAAGCAATTTAATGTCATATATGATATGATTCAGCTTTTGTAGATTTTCAAATATCAGACTATATTCAGTTGTTTATTAAATATGAAAAGATTGATTAAGTCAAACACTTTCAAGCCTCTTTTTCATGAACAAAAACATGAGTAAACACACCAAAGTTGAAAACTCTGACTTTCAACAGACTGTAATTTATGCCTTTCAATCTCCAAATATATTTTTGTAACTGCCTGATGGGTTTATCTTGCCTGCTGCCCAGACAGGGCCTATTTATCCAGACAGGGGAATTGCAAACTCTTTCTCTATGCATACAGTTAGCTGAATAGGAGACTAGAGTTTTATTATTACTCAAATTAGCCTCCACAAAAATTTGGAGGATAGGGTTTTTTAAAGATAGTTTGGTGAGCAGGAGGCTAGGAAATGAGAACTGCTGCTTGGTTGAGGATGCAATCATAGGGGTATGGAAAATGGTCCTTGTGTGCTGATTCAGCTTCTGGCTGGGGAACATGAGGCCAGTTAAATCACGAATCATGGGTCTGAGTGGAGTCAGCTGGTTGTCAGAAATGCAAAAGTCTGAAAAGACATCTCAAAAGGCTAATCTTATGTTCTACGTAGTGATGTTATTTACAGGAGTAATTGGGGAAGTTATAAACATTGTAACTTTCGGAACAATGGCTGGTAATTTTTTACTATGACTACATTTTAGTGGAATTCACACCCCTCTCATAATTCTAACCTTGTGGCTTTGTATTAGTTTTTATAAAGGCAGATTTGTTTGGGGAAAGACTATCATCATTTAAACTATAAAGTACATTTCTCCCAATGTTAGCTTGCTCCATGCCCAGGAACGATCAAGGGCAGTTTGAAGGTAAAAGGCAAGATGGAGTTTATTATATCAGATCTCTTTCACTGTCATAATTTTTTCCCTGTTACAATTTTTGTAAAGGACGTTTCACTCATAAGAATGTTGTTATTCTGTGCCTCAG
Seq C2 exon
GGAGAAGTTGGTCAAATTGGCCCAAGAGGGGAAGATGGCCCTGAAGGACCCAAAGGTCGAGCAGGCCCAACTGGAGACCCAGGTCCTTCAGGTCAAGCAGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718-COL11A1:NM_001190709:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(22.1=100),PF0139113=Collagen=PU(16.8=94.4)
A:
NA
C2:
PF0139113=Collagen=PD(11.8=22.2),PF0139113=Collagen=FE(57.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)