BtaINT0041935 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013760 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chrX:61055343-61057112:-
Coord C1 exon
chrX:61056921-61057112
Coord A exon
chrX:61055630-61056920
Coord C2 exon
chrX:61055343-61055629
Length
1291 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
CCTATCTTCTCTCCTTCCAGGGT
3' ss Score
11.76
Exon sequences
Seq C1 exon
GAGCTCCAGGGAAGCCGGGCCCCTTCGGGAGGGCTGGAGTGCCTGGACAGAGCCTGAGAGTGGGCTACACCTTGGTGAAGCACAGCCAGTCAGAACAGGTGCCCCTGTGCCCCAGCGGGATGAGCCAGCTCTGGGTGGGTTACAGCCTGCTGTTCGTGGAGGGGCAAGAGAAAGCCCACAACCAGGACCTGG
Seq A exon
GTAGGTACCAGCTCCCACAACCACCCCTGGCCATCTGTCCCCACAAGTTCCACTCCTTGTTCCTCCCAACCATTGGTGGGCCCATGTTGGATAGTGGGTTATAAGTACCAGGTCTAGAGTCATTCATGCAGATCTGGGTTCAAACCCTGGCTCTGCCACTTACTCTGGACATGTTATTCAACCTATTTTACCTTCTGCCTCCTTCTCAATGGAACAAGGCTAATTCTAGTACCTGTCTCATAGGTTGGAGTGAGGATTACAAAAATCACCCATGTAAAATGCTTAGAACAGTGTTTTACATATATTTGTTGTTGTTGAGTTGCTAAGTCGTCGACTCTTTGTGACCCCATAGACTGCAGCACACCAGGCTCCTCTGTCCTACACTATCTCCCAGAGTTTGTGCAAATTCATGTCCATGAGTCAGTTATGCCATCTAACTATCTCATCCTCTGTCACCCCTTCTCCTTTTGCTTCAGTCTTTCTCAGCATCAGGGTCTTTTCCAATGAGTCAGCTCTTTGCATCAGATGGCCAAAGTATTGGAGCTTCAGCATCAGTCCTTCCAATGAATATTTAGGGTTGATTTCCTTTAGGATTGACTGGTTTGATCTGCTTGCAGACCAAAGGAGTCTCAAGAATCTTCTCCAGCACCACAATTCAAAAGCATTAACCATCCATTAAACAGTAATGATTAGTGCTAAGGTGCTTAGTCACCCATTTGTATCTGACTCTTTGCGACCCCAAGGATTGTAGCCCATCAGTTTCTTCCATCCATGGGATTTCCAGACAAGAATACTGGAGTGGGTTGCCATTCCCTTCTCCAGGATGTTTCAGACCCAGGTATTAAACCCAGGTCTCTTGCCTTGAAGGCAGATTCTTTACCATCTGAGCCACCAGGAAAGCAATTAGTAGTAGTAATAATAATATGATCTGTGAGTAACAATGATTATCCCAGAATTAACTGAATTGTCTTCAGGTGTGCTGAGTGTGAAATGTAGACTCACTCTATTAAATGTTGGTTTTACAAAATGGGTTGATTTAGGGAGTCTTCATTCAGTTTCTAAAAAGATTCTTTTCATTATCCAATTTCTCTGGTACACAGAAAGTAAGATTTGATCAGCAGACATCAGGGTGTAGTCCAGGACCGGAAGGAGAGGCAACCATGCTCTGGAACAAGCAGTTGGATATGAATCCAAACCACAATCTAGTCCAGTCGTAGTGGCTCCGAGGACAATCCCAGCCTGGTCCCTCAGCCAGACCTTACCTGCTCCTGCCTATCTTCTCTCCTTCCAG
Seq C2 exon
GGTTTGCTGGCTCCTGCCTGCCCCGCTTCAGCACCATGCCATTCATCTACTGCAACATCAATGAAGTGTGCCACTATGCCCGACGGAATGATAAGTCCTACTGGCTCTCCACCACCGCCCCCATCCCTATGATGCCGGTCGGCCAGACACAGATCCCCCAGTACATCAGCCGCTGCTCTGTGTGTGAGGCGCCCTCGCAAGCCATTGCTGTGCACAGCCAGGACATCACCATCCCACAGTGCCCCCTGGGCTGGCGCAGTCTGTGGATTGGGTACTCCTTCCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013760:ENSBTAT00000018292:40
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.231 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(33.8=33.8),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.9=31.2)
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:
CACAGCCAGTCAGAACAGGTG
R:
GATGGTGATGTCCTGGCTGTG
Band lengths:
345-1636
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]