BtaINT0041931 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013760 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chrX:61058828-61060465:-
Coord C1 exon
chrX:61060367-61060465
Coord A exon
chrX:61058975-61060366
Coord C2 exon
chrX:61058828-61058974
Length
1392 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TTTCTTCCACCCTCCCACAGGCT
3' ss Score
11.8
Exon sequences
Seq C1 exon
GCATGAGAGGTGAGCCTGGCTTCATGGGGACTCCAGGCAAGGTTGGACCACCTGGAGACCCAGGACTTCCCGGGATGAAGGGGAAGGCGGGGCCAAGAG
Seq A exon
GTGAGTTGAGAGCATGTTCCTGAGTTCGAGGGAGGGCTTGGAGTGAGATTCTTTCAGGAGTCATTTATCACCGTGCCAGAAACGGAGTTTGTCCACCTCGGGAATACCTCTGCCACCATCAGCTCCCAGGACTGAAGGCCACTGCTGCCTTGCAACCATGAATCCTACCACTGATCTCCCCTCTCTGCATCATTTCTGCATTAGTGTGTACTGGGCTGGCACTCAGTTACCACTTATCCATTTGCTGAATCCAGAAATGAAGCCTGTCTTTTACACCACTCCCCTCAATCACACACATCCAATCCTATTAGCAACTCCTGGGGGCTGTGTTTCCAGAATGGGCCTTGCATCCACTCCCCTCTCATCACCTCCACCAATACCTCTCAGATCCAAGCCACCAACATTTCTCATGTGAATCACTGTGGTGACCTGCTGACTGGTCTCCGTGCTTTCATTATGCACCTCCCCCAACAATCGTTTCTCCAGACTGTGGTGGGAGAGGTCTTATAAAAGCAGAAATCATCCATTGGTATCCCATGGCATCCCTCATCACCAGCTTTTACCCTTTGCTGCTCACTGTGCTTTTCTCACACTGGCCTCTTTCTGTTATCCAAAAACATCACACCCTGGCTGGCCACAGGGCCTTTGCACATGCTAGTTCTACTTCCTGGAATACTACCTCCAGCCCCTTCTAATGCTTTAATAATCTCAGCTTAGGTGTCACTGATTGTAAAAGGCCACTTATCACTAAAGCAGGTTCTCTCGGAGAAGGCAATGGCACCCCACTCCAGTACTCTTGCCTGGAAAATCCCATGGACAGAGGAGCCTCGTAGGCTGCAGTCCATGAGGTCGCTAAGAGTCGGACACGACTAAGCAACTTCACTTTCACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAACCCACTCCAATGTTCTTGCCTGGAGAATCCCAGGGACGGGGGAGCCTGGTGGGCTGCCATCTATGGGGTTGCACAGAGTCGGACACGACTGAAGTGACTTAGCAGCAGCAGGTTCTCTACCCTGTAGCCCTCTCTGCTCCATCCCACAGTCACTGCACTCTCCATTTCCTTTGTAGCACTTTTCACAATTTGCAGTAAGGTTAATGGTTTTTGTCAGGTTATGCATATTTCATCTTTATCAACAGACCATTGTCTCATAAAGGTCTTACTCACTGCTCTATCCCCTCATCTACCAGGGACTAGAACTCAGTAGGCACTCAAGCAAATTGACTTATTTGGCTTCTATCAATAAGCCAGCTGGTTGAGTTTGAGGTCCTAGGCTGTGATGCCAACTGAACCTCCAGGGGCCTTCCCTAGCCACCTCCTCTGCCTCTGCCTGACATTTCCGTTTCTTCCACCCTCCCACAG
Seq C2 exon
GCTTATCTGGCCCTCGAGGTGCTCCTGGACACACACCCATTGCAGAAGCCATCCAGGCTCCCCCTGGACCCATGGGTCTTCCAGGCATTGATGGAATCCCTGGCCTCATGGGAGACCCTGGGGTCCAAGGACCTGTGGGCCTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013760:ENSBTAT00000018292:37
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(52.4=100),PF0139113=Collagen=PU(11.5=29.4)
A:
NA
C2:
PF0139113=Collagen=PD(22.2=28.0),PF0139113=Collagen=FE(56.3=100),PF0139113=Collagen=PU(4.6=6.0)
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:
AGGTGAGCCTGGCTTCATGG
R:
CTTGTAGGCCCACAGGTCCTT
Band lengths:
239-1631
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]