BtaINT0041726 @ bosTau6
Intron Retention
Gene
ENSBTAG00000025210 | COL4A2
Description
collagen, type IV, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2203]
Coordinates
chr12:89160505-89160886:+
Coord C1 exon
chr12:89160505-89160666
Coord A exon
chr12:89160667-89160787
Coord C2 exon
chr12:89160788-89160886
Length
121 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGTA
5' ss Score
-0.35
3' ss Seq
ACGCCCTGCTTGTCCTGAAGGGC
3' ss Score
6.04
Exon sequences
Seq C1 exon
GTTATCGAGGGCCCCCGGGGCCGCCCGGGCCTGCAGCTCTCCCCGGAAGCAAAGGCGATGAGGGGAGTCCAGGAACCCCCGGAAGCCCCGGGACCAAAGGATGGATCGGCGACCCCGGGCCCCAGGGCCGGCCTGGCGTGTTCGGGCTCCCAGGAGAAAAAG
Seq A exon
GTTGTAACATGGGTGGTGTCCCAGGAGGAGGGAGGGCTTCTCTCGGGGACACTGGTCAGAGATGGCTGGAGACCCCCCTGCACCAGGCCCGCATGTCCTCAACGCCCTGCTTGTCCTGAAG
Seq C2 exon
GGCCCAAAGGGGAGCCAGGATTCATGGGCAACATAGGCCCCACCGGGAGCCCGGGCGACCGAGGCCCCAAGGGACCCAAAGGAGACCGAGGACTCCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000025210:ENSBTAT00000005916:39
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(73.0=83.6),PF0139113=Collagen=PU(23.1=27.3)
A:
NA
C2:
PF0139113=Collagen=FE(50.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTATCGAGGGCCCCCGG
R:
GAGTCCTCGGTCTCCTTTGGG
Band lengths:
257-378
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development