GgaINT0039355 @ galGal4
Intron Retention
Gene
ENSGALG00000005180 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr8:10281743-10282440:+
Coord C1 exon
chr8:10281743-10281850
Coord A exon
chr8:10281851-10282386
Coord C2 exon
chr8:10282387-10282440
Length
536 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
CTGTCCTTATTCTTTCTTAGGGA
3' ss Score
10.61
Exon sequences
Seq C1 exon
GGACATCCTGGTTTGATTGGCCTGATTGGACCTCCAGGAGAACAAGGTGAAAAGGGTGATAGGGGTCTTCCTGGTCCACAGGGGTCTCCTGGAGCCAAAGGTGATGCA
Seq A exon
GTAAGTAAAACACTCTTTTGCTTTCATTCAAGTTTCATGTATGTCTTTCTTGCAGGAGACACATGAAGTTACTATAAACATTGATACTCAGAATCTCCAGCTGGAGTTTAAAGCTTTCATAGGCATTGTATAAACACAAGGTAAAACCAGGACACAGATTGTTGATGAAGGAAACAGTATACCTCTGTTAGGTATCAGATAACTACCAGCGCCAGTCTTGTTACATACTACCCAAAGCAAACTCTCTTTTCCTGGTTATTAAGCTATGTTTTAAAACTCTCTGTAAAATATGAAGCTTTAACGTTTATCTGAAGGAGAACAGTGTTGTGACTATAAATGCTGGAGCATGAGAGACACTAAAACTGTCAGATTGTATTTTAAATTTAAAAATTATTTTGGACCCTAGCAAATGGACTAAAGGGAAACTTTAGTTTCAGGGGTGGGCACTTAGTAGGACTACCATTCTCAATAGATCTACATTTCTTAACTCAGTCCAGTACAAAAAATACTTTAATTCTGTCCTTATTCTTTCTTAG
Seq C2 exon
GGAATTTCTGGTCCTGCTGGTCCACTCGGACCCCCTGGTCCTCCTGGTTTACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005180:ENSGALT00000008321:59
Average complexity
IR
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=PD(7.9=16.7),PF0139113=Collagen=FE(50.0=100),PF0139113=Collagen=PU(3.3=5.6)
A:
NA
C2:
PF0139113=Collagen=PD(21.4=83.3),PF0139113=Collagen=FE(28.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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]