BtaINT0041936 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013760 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chrX:61054247-61055629:-
Coord C1 exon
chrX:61055343-61055629
Coord A exon
chrX:61054655-61055342
Coord C2 exon
chrX:61054247-61054654
Length
688 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
CCACCCTCTGTCCGTTTCAGCAC
3' ss Score
10.03
Exon sequences
Seq C1 exon
GGTTTGCTGGCTCCTGCCTGCCCCGCTTCAGCACCATGCCATTCATCTACTGCAACATCAATGAAGTGTGCCACTATGCCCGACGGAATGATAAGTCCTACTGGCTCTCCACCACCGCCCCCATCCCTATGATGCCGGTCGGCCAGACACAGATCCCCCAGTACATCAGCCGCTGCTCTGTGTGTGAGGCGCCCTCGCAAGCCATTGCTGTGCACAGCCAGGACATCACCATCCCACAGTGCCCCCTGGGCTGGCGCAGTCTGTGGATTGGGTACTCCTTCCTCATG
Seq A exon
GTGAGGCACCACACTGCCCCTTCCCCCAGGGTAAAGGCCGAGGGTAGGGAGTGCTTGGAGGGAAATCCTGAAATCGAGTGCTGAAGGAGCTGGGTGACACGAGGGCCAGAACTTTAGGCCAAATATGAGGCTCATCTGTACTCAACAGGTGACACGCCCCCTCATGGCCGTGGTACAGATTGCAAGTAAGAGTTCCAATAAAGGTGACTTCAGAGTAGGAGCTGTTAACAGATCCATGAGGGGATGGGCCCATGGTCTAACCCCCTGGTAGACTATTCCATGCTCTCTCCCTTCTCTGGAAAACACCATCATGGGCTTGGAGCAAAGGGTTCTGAGAACTGCATTCTGAATCCCACTGAATTTTCTTTAATTCAGCCTTTCTCAGATTTCTTCGTCAGTGGAAATCTGCCAGGGGCACTAGCATACTTGGGGGACTTGGCGGGCATCAGCAGTCTGAGAGAAGCTGTCTAGCATGTAGCCACAGCCCAGGAACTGTGGGCTAGGAGGGCACTCGGGAGCTCAGAGGGGGCACTCCTGGCCCTGAGGCGGTGACAAGGATCCAAAACACAGTGTTTGGTTTATTGACCTGACATGGGGGCTGAACCAAGGGACCGGAGCTCAGGGCTGGAGAAGCAGAGCCTGTTGGCTCCCAGGTGACCAGCTCACGGCCACCCTCTGTCCGTTTCAG
Seq C2 exon
CACACAGCCGCCGGTGCAGAGGGCGGGGGCCAGTCCCTGGTCTCTCCCGGATCCTGCCTAGAGGATTTCCGGGCTACTCCTTTCATCGAATGCAGTGGTGCCCGGGGCACCTGCCACTACTTTGCCAACAAATATAGTTTCTGGCTGACAACAGTGGAAGAGAGGCAGCAGTTTGGGGAGGAGCCTGTATCTGAGACGCTGAAAGCTGGACAGCTCCACACCCGAGTCAGCCGCTGCCAGGTGTGTATGAAAAGCGTGTAGGGTGGCACCTGCCACTCTGCCCCATGCCCTCCCCTCCTGCACACAACGGTCACCTCACAAACCCGAATGGTCTGAAGAAGGAAGGCCTAAGCCCTTTTGCCCATCTGTCAAGCTGCACCTTGGAGTCTCGTTTGGGCTGGACTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013760:ENSBTAT00000018292:41
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.023
Domain overlap (PFAM):
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.9=31.2)
A:
NA
C2:
PF0141314=C4=PD(72.4=96.6)
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:
CGCAGTCTGTGGATTGGGTAC
R:
TTGTGAGGTGACCGTTGTGTG
Band lengths:
354-1042
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]