GgaINT0068164 @ galGal4
Intron Retention
Gene
ENSGALG00000008141 | COL4A5
Description
collagen, type IV, alpha 5 [Source:HGNC Symbol;Acc:HGNC:2207]
Coordinates
chr4:13890702-13891216:-
Coord C1 exon
chr4:13891119-13891216
Coord A exon
chr4:13890853-13891118
Coord C2 exon
chr4:13890702-13890852
Length
266 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTGT
5' ss Score
6.43
3' ss Seq
TTCATTTAAATTTGTTACAGGGG
3' ss Score
7.43
Exon sequences
Seq C1 exon
GTTTCCCAGGGACTCCAGGCCCACCCGGAGCTCCAGGAACTCCAGGTCGCCCTGGCCTAGATGGACCTCCTGGACCACCTGGTTTCCCAGGCCAGAAG
Seq A exon
GTCTGTGCTTGCTCATTTAATATAAAGCTTCATTTTATTGAAAGCTCTTTTGCATCTGTGAAGTTGATAGGTAGGGAGGTTCTCACCTCTTGTTAGCTTTTCATGGTAAGTCACATTCTCTACTTGAAGCTTGAATGAGTGTAGACAAAAACAAACTGAATTCTTGAGATGATGTGTGTTTTTTCTTTACTGCTCTAGCATTTCTCTGGAGAGGCTAAACTCAGAAACCTTTCTTTTTAAAATCTATTCATTTAAATTTGTTACAG
Seq C2 exon
GGGGATCGTGGATTTGGAGTTCCAGGACCACCTGGACCCCCAGGACCACCAGGCATAAAAGGAGTTCAAGGACCTAAAGGTGATCCTGGCTTCCCAGGAAACCCTGGTCTTCCAGGACGGGCGGGTTTTGATGGAACTCCAGGACCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008141:ENSGALT00000013221:28
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=FE(57.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(32.1=35.3)
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:
TTTCCCAGGGACTCCAGGC
R:
TGGGTCCTGGAGTTCCATCAA
Band lengths:
245-511
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]