GgaINT0032136 @ galGal4
Intron Retention
Gene
ENSGALG00000004946 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr9:8818772-8819581:-
Coord C1 exon
chr9:8819477-8819581
Coord A exon
chr9:8818937-8819476
Coord C2 exon
chr9:8818772-8818936
Length
540 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
TCTGTATCACTGCTTTACAGGTC
3' ss Score
8.55
Exon sequences
Seq C1 exon
GCCCACCAGGAGATCCTGGATTTCCAGGTCCTGCGGGTGACATGGGGTCAGTTGGACCTTCTGGCCCTGTGGGTATGCTAGGAAGACCAGGAGACGATGGAACAA
Seq A exon
GTAAGAGATTTTGGGAACAAAATAATAACTCTATACCAGTAAGAGAGAACTAAAAGAAAACTCTTTGTTCTGGTTTCATGCAAGTCACCAACAATAAGGATTTGGGGTCCACAGAAAATGAAAAAAAAATATATATTATCCCAGTACTTACTCATACTAAAAAAAGAACCAAAATGTTCCAAATAGAGCATTAGGAGTTGCTAGAAAATGAACAGAAGGCAGAGCAGAAAATGCTGCCATGTACTGTATATCCATGGTGTACCTGTATCTGTAGCATTGTGCTCAAAAATCCTGTTCACAACTTCAAAAAGTTGTAAAGGAGATGATATAGATGACTTGGCTCTATATAAGGACCAACTGAATAAACTGATGTCTGGACAGATAACGAGGAGAAGGAGAAGAGGCATTTGAAGGTACAAAGCAGAAGCCACTTGTGTTTCCTGGGGAAAGAAAACATAAGTATTTAGATTTAAGTCTTATTTATCGAACAGAGTCTCTTCTGCATGACAGTTCTGAATTGTCTGTATCACTGCTTTACAG
Seq C2 exon
GTCTGCCTGGCCTGCCAGGAATAAGTGGGGCACCAGGACCTCAAGGTTTTCAGGGTGACCCTGGTTTGCCTGGAACAGGTGAAGCAATTCCAGGAAGACCTGGATTTCCTGGACCACCTGGACTACCAGGACAGCCAGGAAGACAAGGCTTACCTGGACTACCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004946:ENSGALT00000007918:19
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(41.7=100),PF0139113=Collagen=PU(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=PD(31.3=46.4),PF0139113=Collagen=PU(90.2=98.2),PF0139113=Collagen=PU(28.2=42.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGATTTCCAGGTCCTGCGG
R:
TAGGTAGTCCAGGTAAGCCTTGT
Band lengths:
254-794
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]