BtaINT0041813 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021310 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:116057943-116059416:-
Coord C1 exon
chr2:116059357-116059416
Coord A exon
chr2:116057988-116059356
Coord C2 exon
chr2:116057943-116057987
Length
1369 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
GATTTTTGTGAATTTATTAGGGG
3' ss Score
4.47
Exon sequences
Seq C1 exon
GGAGAGCCTGGTATTGGGAGAAAAGGAGAGAAAGGGATTCCTGGGTTTCCAGGACCTCGG
Seq A exon
GTAAGGCTCCTTCCTGCTCTCTTGAACTTAAGTGAGTTTGGAGGCATTTCTCTTTCACATTTTTATAAGATTCAATCAATAATTCTGAGAGCTCAAAAGTGGAGATTTTCTCAAAGAGGAGTACTGTCTTGCTCAGCAAGAATTGTGTGATAGCTAAAGGTCCCAGAGCATCCCTTCTGTGCACATCATTTGGATAAAACAGGCAAGCAAAAGATGGGACAATTGGCAGGAAGTAATGGGATCATGGTCAAAGCTCTGATTTTTCCAGTAGTCATATGCAGATGTGAGTGACGGACCATAAAGAAGACTGAGCACTGAAGAATTGATGCGTTTGAACCGTGGTGTTGGAGAAGACTCTTGAGAGTCTCTTAGACTACAGGGAGATCAATAGTAGTCAATCCTAAAGAAAATCAGTCAATCCTAAAGAAAATCAACTCTGAATATTCATCGGAAGGCCTGATACGAAGCTAAAGCTCCAATACTTTGACCACCTGATGTGAAGAGTCAACTCATTGGAAAAGACCCTGATGCTGGGAAAAACTGAGGGCAAACGTGAAGGGAGTGACAGAGGATGAGATGGTTGGATGGCATCCTTGACTCAATGGACATGAGTTTGAGCAAACTCTGGGAGGTAGTGAAGGACAGGGAAGCCTGGCGAGCTGCAGTCCATGGAGTTGCAAAGAGTTGTACACAACTTAGAGCTAAACAATAACAAAAATGGGATCATGACATTTTCTCACTGGCTCAGTGTCAGTGTGATTGTAGCTTGGAATTGTTCAGTTAAGCCTATTTGACAAAAGAAAGTACTGATCTATGGATAGTAGCTAGAAAAAAAAAGTACAGCATCAGGCCTCAACATCTCCATACCTGTCACTAATGGGATCCCCATTCACAGAGTCACAATGAAGGCCAGACCCCAACAGCCATGGACACTGAGTTTATTTGACTCCAGATTTAGTACTTAATGAGGCAATATTAACTTCCATAGTAATTTTTATTGCTGATAATGCATAGAGCAACTATTAATCTCCAGACAAATTATATTGCAATGATTCAAAGATATTTAGCTCAGTGAAAGCATTACATTAAATAAATTAAAGTGGAAGAGCAATACAAACAACAAAACTATATTCTTAATTTATATCACTGGAGAGGACATGATTTTTTTTAATAATATTAAAGAGTAATTAAAATAGCAAATGTTGTAAAGAAATGGAATCTCTTTTATGTTTATTTCCTTTATTCAGTTATCTTTGTAGGCATGATTAAAAATCCCAAAAGCAATCTCATAAGGGGAAAAATGATTTACTGAATTGGTTTATGTATTTTTATTTAACTTTGCTTGCGTTGATTTTTGTGAATTTATTAG
Seq C2 exon
GGGGACCCTGGTTCCTATGGATCTCCAGGTTTTCCAGGATTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021310:ENSBTAT00000018302:16
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(21.6=100),PF0139113=Collagen=PU(21.5=70.0)
A:
NA
C2:
PF0139113=Collagen=PD(13.6=80.0),PF0139113=Collagen=FE(21.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]