GgaINT0068178 @ galGal4
Intron Retention
Gene
ENSGALG00000008141 | COL4A5
Description
collagen, type IV, alpha 5 [Source:HGNC Symbol;Acc:HGNC:2207]
Coordinates
chr4:13869755-13870363:-
Coord C1 exon
chr4:13870230-13870363
Coord A exon
chr4:13869828-13870229
Coord C2 exon
chr4:13869755-13869827
Length
402 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAA
5' ss Score
6.68
3' ss Seq
CATGAATCTGTTGTCTTCAGGGA
3' ss Score
7.75
Exon sequences
Seq C1 exon
GTTCACCGGGCCCAGAAGGTCCACGAGGGCCACCAGGCAGTGGGGGACTCAAAGGGGAAAAAGGGAACCCAGGACAGCCTGGCCCACCTGGCCTGACTGGTCAAAAGGGAGACCAAGGACCACCTGGACGCCAG
Seq A exon
GTAGAACAAGAATTGGGTTTATTTTTAAATGCAATAAAAACTGAACATGTTTAGGTTAAATATGCCTTTTATTGCAGTAAAATAAAACACAAAATATAGTGGTGGTTATAATCTGTCTCATAGCAAGATGGAGGGTCTTTTATTTATCCTCCAGTACCCAGGCAGGTTTTCCCCATTATATTGCCATGGGAGCTGGATTTGCCAACAAGGGTTCGCATTCCTGTGTTCTCTGATGGCAATTGCAGTACCAGGCAGTGAGCAAGCAAAATACAAGGCCTCAGCCCTCTCAAGCACTACTTCACAGATCCAAAATGTACTAATTTGTCCCCTACCCTCTGTTTTCATCTTCTTTTCTGAAACCACTGGGGAGATGAGTGACTAACATGAATCTGTTGTCTTCAG
Seq C2 exon
GGAGATCCTGGTCGTCCTGGTCTCAATGGAATGAAGGGTGACCCCGGGGTTCCAGGCGTTCCAGGATTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008141:ENSGALT00000013221:44
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(55.2=71.1)
A:
NA
C2:
NO
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:
GTTCACCGGGCCCAGAAG
R:
CTGGGAATCCTGGAACGCCT
Band lengths:
207-609
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]