GgaINT0039302 @ galGal4
Intron Retention
Gene
ENSGALG00000005180 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr8:10199801-10200644:+
Coord C1 exon
chr8:10199801-10199917
Coord A exon
chr8:10199918-10200548
Coord C2 exon
chr8:10200549-10200644
Length
631 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACA
5' ss Score
8.1
3' ss Seq
TACTTTTTCTTTAATATTAGGCA
3' ss Score
6.36
Exon sequences
Seq C1 exon
TACACACCAGAAGATTTTATCGAATATGACTATGAGTATGGGGATGCAGATTATAAAGAAACTGAGTCTGTAACAGAGGGACCCCCACTGTTTGAAGAGACAATAGCACAAACAGAG
Seq A exon
GTAACAGAATCTGATCTGTTTGTTGTCTGGTGTCCAGCTGTCCCTTACCATGTGGTTTGTCAATTTGTGTCATCTATATGTAAGCTTAATGTTTTTCTTTTACTCATTTCTTTACTCTTCAGCTTTAACACTTGCTTTTACTTAGCTATGGAAGGCCTCACAACTGAGAGCATTCATCTCAAATTCATATACGCTTCGTTCAATCATTCCTTCATTCCTTCATTCATTCATTCATTCATTCATTTTCTTTTCATTTTCTTTATGTTTTCCCATTCCATCTTTCATAACATTTGCAGAAAAGGAAAGCCATGGTCAAAAAGAAGAAGAGGACAGTGGCCACTAGCTCAAAGGACAAATCCCAAAAGGCCACAACAAAAAAATCTGAAAAATATGCATCCAAGAAGAAGAAAAGTTATCAAGCAGCAACAAAAGACAAACTAGGGGTAAAAGTAGCAAAGAAAAAATCAAGATCTTTCCCAGGCCAAGAGTGGAAGATCTCTGATGATGAGAAAAAAATAGACAGCTCCACCAGATGAATATCTGGCTTATAACATAACCTGAATAAAAGTGAGACTTCTTGATTTTTCCTACAGGATTTTTTTTTAATAATGTACTTTTTCTTTAATATTAG
Seq C2 exon
GCAAACATTGTTGATGAATTTCAAGAATATAGCGTAGCTGGAAATGACTATGGGCCCCGGACAGAAGCACCCTCCAGAACTACTGAAGCCAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005180:ENSGALT00000008321:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.846 A=NA C2=0.938
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACACACCAGAAGATTTTATCGAATAT
R:
GGCTTCAGTAGTTCTGGAGGG
Band lengths:
206-837
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]