GgaINT0105266 @ galGal4
Intron Retention
Gene
ENSGALG00000016843 | COL4A2
Description
collagen, type IV, alpha 2 precursor [Source:RefSeq peptide;Acc:NP_001155862]
Coordinates
chr1:138380991-138381382:+
Coord C1 exon
chr1:138380991-138381152
Coord A exon
chr1:138381153-138381283
Coord C2 exon
chr1:138381284-138381382
Length
131 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CGTGTCTTTTTGCATTAAAGGTC
3' ss Score
8.91
Exon sequences
Seq C1 exon
GCTATCCAGGACTACATGGGCAGCCTGGAATACCAGCTCCACCGGGAAGCAAGGGAGAAAGTGGACGAGCAGGTGTGAGCGGACAAGCTGGCCCCAAAGGGACAAGAGGTGATCCTGGATTACCAGGGAGACCTGGGATTCCTGGTTATCCTGGACCAAAAG
Seq A exon
GTGAGGATGGGAGATGCTGATCATCTGTAGAGGGGAACCCTCTGCGCTACAACAGTTTGAGTATCATGACTTCAGAATTCATGTGATCTGTGTTAAAATACAATAATGTCACGTGTCTTTTTGCATTAAAG
Seq C2 exon
GTCGTAAGGGTGAACAAGGTGTCATTGGCTTTATTGGCACAGTAGGATTTCCAGGTGATTTGGGACCCATCGGACCCAAGGGGGATAGAGGGCTTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016843:ENSGALT00000027208:41
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(66.7=100),PF0139113=Collagen=PU(24.6=27.3)
A:
NA
C2:
PF0139113=Collagen=PD(11.1=26.5),PF0139113=Collagen=FE(54.1=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:
ACTACATGGGCAGCCTGGAAT
R:
TAAGCCCTCTATCCCCCTTGG
Band lengths:
248-379
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]