GgaINT0032150 @ galGal3
Intron Retention
Gene
ENSGALG00000004946 | COL4A4
Description
NA
Coordinates
chr9:10399465-10400323:-
Coord C1 exon
chr9:10400145-10400323
Coord A exon
chr9:10399529-10400144
Coord C2 exon
chr9:10399465-10399528
Length
616 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
AAAAAAAATAAATAAATCAGGGT
3' ss Score
-0.13
Exon sequences
Seq C1 exon
GTGAAAAAGGAAATACAGGTTTCAGAGGTGCCCCAGGATTTCCAGGTAACAACGGTGCCCCAGGACTTCCAGGTGACCATGGTGACATTGGACTGATGGGATTTCCAGGATCACGTGGTTTCCCAGGACCAAAGGGCTCTAAGGGAGTTACAGGTTTCAAAGGACTACCAGGTGACCAG
Seq A exon
GTAAATTGAAGTGACAGTGACAGTCCTGGACTTTAGGTACATCTCTCCCAACTCCAAGAAATACAATAGTGGATACTCATGTTGAACTTGAAGTTGCTTTTTGGTACGAGGACGTATATTTGCTTATCTTGTCCTTTATTATATTTCTTTGAAGAGAGAATCTGCTGTGCTGATTATTTAAAAGGAAAAATAAAGAAATCCTAATATTTTGATTGTTACATCACAACAGATTTTCGGTTAACGTTTGTAGTAAACTGGGGGTAAAATACAATAATATTTGGTACACCATTGTAGTACCTTTAAAATTAAATTCCTCAAACCACCTGTAGGGAATTGAAGATGTTAAAGCAAAGCCAAGCATTAGCATAAACAATTTCAAAATTGTTAGTAATTCTAACATAGAGTTTTTTGGAAGTGTTAATCGTCAGTGTTAGATACGTAATGAAGACAGCATGCTTTTCTGTTGGGCTTAAGATACAGTTTTGCTGTTCATATTGATTTCCAGTCTGTTTGGCAGTGTAAAAGAACTAAATATTTTTACAGATCATTCTTATTACACATATCATCCATCAAACTTTTTTTTTTTTGATTGCTCTAAAAAAAATAAATAAATCAG
Seq C2 exon
GGTGATGTTGGCTCACCAGGAATGCCTGGAAACCCAGGACTGACAGGCCCCAAAGGACCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004946:ENSGALT00000007918:33
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(60.0=55.0),PF0139113=Collagen=PU(52.5=53.3)
A:
NA
C2:
PF0139113=Collagen=FE(34.4=100)
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:
AGGAAATACAGGTTTCAGAGGTGC
R:
GTCCTTTGGGGCCTGTCAGTC
Band lengths:
230-846
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]