BtaINT0041833 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021310 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:116018007-116019087:-
Coord C1 exon
chr2:116018906-116019087
Coord A exon
chr2:116018071-116018905
Coord C2 exon
chr2:116018007-116018070
Length
835 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
CTGTTTCATTAAACTATCAGGGT
3' ss Score
5.3
Exon sequences
Seq C1 exon
GTGATAAAGGTCATCCTGGGATGCAAGGAAGGAGAGGAGAGCCAGGAAGCCATGGACCACCTGGATTTCACCCTGGGGAGCCCGGAAGAAATGGACAGCCAGGGCTTCCTGGACCCCCAGGCCCTCCAGGCTCACCTGGGCTGAGAGGAAACATTGGTTTTCCAGGATTTCCGGGTGACCAG
Seq A exon
GTAAGCAGCTGCTGTTTTGGAAGGAAAGAAATAATAAAACCTTTCTGTCCTGGGGATGCCCGTTAGGCATCTTACTTTGCCAGTGTATGTCAGGGTCCTTTCAACAGCTTTTAGAATATAAGAAGTTGGTCAAGAGAAGAATGGAGACTCTGGAAGGCCATGATGTAACTAATTTCTGACCAGTGCTCATGCCTGGTTCCAGGCGTGATAGATGATCAAGTCACTTACTCCGCATACTACCCCTCCTTTGTTTAAACAGCTTCAGAAAGACTTGCCTCAGGACTGCTGGTTCACCAGATTAAAGAGTCATGTGAAAAAATGACCCAATTTCTGCTTTCAAAGCCTTCCTATCTGATGGCAGATATCATAGATTTTGTTGTAAATATTTTTTATCTTTACAATCATGAGCCGAATACCCCAGGAAGTACAGCTGTAGGAGCCTAATTTACAACTTCTGGAAAAATGTATAGCATACTCTGCTACTCATTTTTTGGAGTAAAATAGATTTTTAAAGCTTTATAATATTTTATTTGGTATCAGTTCATTCATTCAAAACTTAAAGTTCAAATGATGTGATGCAATTACTGTTTTACAATCAAATATAGAGAATTGGATACCTCCTGTTGGTATCACTACTTCTGGAAGCATTTTGCCAACTTTTTACAAACTAGATGTATGCAGTGATATGCTTGCAATCCATTTCCAATTTTCTTTACCACAGCAAATTATAAAAGCCAACTTTGTTATAGAAAATGATAACTGGGTCATGTCAAGAGTGTGTCATTTGTATTTGAAATTCGGTTAAAGTCTTACTTCTGTTTCATTAAACTATCAG
Seq C2 exon
GGTGAGCCAGGTTCTCCAGGGTGCCCGGGACCTTCAGGAATGGATGGTACAAGAGGACCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021310:ENSBTAT00000018302:34
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(62.7=60.7),PF0139113=Collagen=PU(54.4=60.7)
A:
NA
C2:
PF0139113=Collagen=FE(30.9=100),PF0139113=Collagen=PU(8.5=27.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGATAAAGGTCATCCTGGGAT
R:
CTTTAGGTCCTCTTGTACCATCCA
Band lengths:
246-1081
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]