GgaINT0032141 @ galGal4
Intron Retention
Gene
ENSGALG00000004946 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr9:8813942-8814664:-
Coord C1 exon
chr9:8814558-8814664
Coord A exon
chr9:8814126-8814557
Coord C2 exon
chr9:8813942-8814125
Length
432 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
CAACAGCTGCTTTCTTTTAGGGT
3' ss Score
7.05
Exon sequences
Seq C1 exon
GAATAAAAGGTGAAAGAGGTCCTACTGGGGTTCCAGGATTTCCAGGCCAAAAAGGTAATGATGGCAGAGATGGGGATTTAGGATTGCCTGGGGAAAAAGGAGATGAG
Seq A exon
GTATGTTTGACTTTCTCAGGACTTTTTTCTATATGGGTTAACATTTTGTCTTAAGGGACTATCTCTTAATGAAAAGTGTAATCTTATTCCAAATTCATAGCAGATTAATCACTTTTATCATTTTCTGTTAGTCTAGATCAAAAATCATACTATCACTGAAAAAATTATTTCTTTGGAAGTAGTGCTGCTTATTTTGTTACTTCTGGATATATCTAATGCATATACTGGATCAATATGGTGGGATCAGAAAGAAAAGGTCTACCTTCTGTGCCTGTTGTTTTTCATTATCTGGACTAATAATGTCGCCCACGTAGTTTCCTGACTGCAAAACAGTGTTTTCTGCAGATAATTTTCTACTTGTGGCTTTCAATAATCAAAGAGAGGAAAGGAGTTAGGCCATGCTATTTCTTGTCAACAGCTGCTTTCTTTTAG
Seq C2 exon
GGTGATTCTGGAGTACCAATACCAGGTGATAAAGGATTTCCTGGAGTTCCAGGACTCCCTGGAGTAAAAGGACCAATGGGATTGCCTGGTTTGGGGTTTCCTGGCCCTCCGGGAGTTAGAGGTACCCCTGGAGACTTTGGTGATGATGGTAACATTGGTCTGCCTGGTCCAAAGGGTCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004946:ENSGALT00000007918:24
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(46.7=100),PF0139113=Collagen=PU(20.5=47.2)
A:
NA
C2:
PF0139113=Collagen=PD(9.5=11.3),PF0139113=Collagen=PD(52.5=50.0),PF0139113=Collagen=PU(93.2=88.7)
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:
AAAGGTGAAAGAGGTCCTACTGG
R:
CTTTCTGACCCTTTGGACCAGG
Band lengths:
286-718
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]