BtaINT0041917 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013760 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chrX:61075198-61077023:-
Coord C1 exon
chrX:61076862-61077023
Coord A exon
chrX:61075369-61076861
Coord C2 exon
chrX:61075198-61075368
Length
1493 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TCTCTCCTGTGCTGATTCAGGAT
3' ss Score
9.84
Exon sequences
Seq C1 exon
GTTTGCTTGGGAAGTCGGGCTTGCTCGGCCCCAAAGGTGAGCGGGGCAGCCCTGGAATACCAGGCCGTGTGGGTCAGCCAGGACCCCCAGGCCCTAGTGGTCTATTTGGCATCAAGGGCAAACCCGGGCTCCGCGGACCCCCAGGCTTTCCAGGCATTTCAG
Seq A exon
GTAGGTCCTTCAGAGGAGCAGCCACAATTTGACAGACAAGCTGGGCCCTGGGGCCCTAGCACCCTGAGGGGCAGTAACAGCAGTGTGACAGGGTCAGAGCCGAGAAGGAGACTGAGTTGTCTTACCTGAGTTTCACATCTCAAGCCCCCTATGGTGCCAGGTTGAACCAGTTTGGCCTCCAAAAAGTGACCCTCAAATATGAGCACTTCTCGCCCCTCCCCCATGGCCTCCGCCCACCCACCCACAGACCCCACCCCTGACCCTGGCAGCCTGCCTCTTGGGCCAGCAGGTCTCTGAGGACCCAGGGCCAAAGTGTTTTTCACTCCACAGTGGGGCGTGACATCCCCTGGTTCCAGCCTAGTGTTTGCAACTTGCCTTTTTCTCACACCACCCTTTTCACCCCTGACTCCTGGCCACGTGACTGAAGTTGAGTTTGTATACAACTATTAATATCTTTTTTAATCCTCTTTGTGGTTGTGTGTTTCTGGGGTCTTCACATAGGCTGTCCAGGTGAGAAAACAGCACGCAAGCTCACAGACTAACACCCCCACCAGCTTGGCCTCTCAGGGAATTATCTTACTATACATTACAACCTGGTAAGGCCAGGGGTCCCTGAACTCATACTGTGGGGTTGGCCCCCATTGACTTTCCTTCCCTTGTTGTGGAATCCCCTTCACAGCCTCCCATTAGAATCCTGGGGCTCCCAGCTACATGATGCTTTTCAATCCATAGAAAGCCAAGCCAGCCATTCATTTAGGTCCTTGGGGGCCCAAATACCTCTCTCATCACTGATTTGATCCTTTGATTTTTTAATTTCCTTGCTTTGTACCTGAACATTCCACTTTGGCAGCAGCTCAAGAGGTTAATCCCATTGAGTAACTGAAAGCCTGGTGAAAGAAGTCTCAGAATACCTAGGAGACCAGATGGGCCTTGGGAATTTCTACAGTACTTGGCACTAGGGGGTCTTTCAACTCTAATGCCAAGGAACTGGCTGACTTAACTGCTTGCATGAGGGATTAAAAGGGCAGCCCTGATCCATGACTCCCTGGGAGGCTGCAACAATTGTTGGGCTTTAACCTCTACTTCACCAGTTGGCTCAGGAAACAGCCATTGTGGACTGATTCATGCTGGAATTACCAGGAAACTAGAGTCCACTTGCCACCCTGGCTCCCTAGAGCTCCATTCAGAGGCTAAAGTATGAACCACATTCATAAAGGGAGAAGAGTTGTCATCAGAAGGGGTTTGCTCATCCGCCCTGCCAGCTATAGTGCCATGCTGGTAAAGGTAGCCACTGTGGGGCATCCTGGGTGACAAGTGCTATGCATCAGCCAACTGAAAACCACTCTTCCTGTTAGCCTGCATGGCCCATTGTTCAAAGGCTGTTTACAAACCCCAACAAGTCAACCAACAAGAAGCCAGGGGAATGGGCAGTGGCCCAGATCTGGATAGTCTCACTTGACAGCCATCATGTATTCTCTCCTGTGCTGATTCAG
Seq C2 exon
GATATCCTGGAAAGAAAGGTCCAAGAGGCGAGATAGGTCTCCCTGCGTCAGCTGGAAAGAGAGGCCTGCCTGGGCTGAAAGGGCTTCCGGGACTGCCAGGGCCAATTGGCTTCCTGGGGAACTCAGGCTTGCCAGGGGCCACTGGGTTACCAGGCCTGCCAGGTCTGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013760:ENSBTAT00000018292:24
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=PD(47.5=52.7),PF0139113=Collagen=PU(53.8=76.4)
A:
NA
C2:
PF0139113=Collagen=PD(44.9=60.3),PF0139113=Collagen=PU(65.8=82.8)
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:
TTTGCTTGGGAAGTCGGGCTT
R:
CTTCAGACCTGGCAGGCCT
Band lengths:
331-1824
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]