BtaINT0041868 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014575 | COL4A5
Description
collagen, type IV, alpha 5 [Source:HGNC Symbol;Acc:HGNC:2207]
Coordinates
chrX:61750318-61751476:+
Coord C1 exon
chrX:61750318-61750509
Coord A exon
chrX:61750510-61751307
Coord C2 exon
chrX:61751308-61751476
Length
798 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
ATTAACCTTTTCCCTTTCAGGGT
3' ss Score
12.2
Exon sequences
Seq C1 exon
GGCATACCAGGAGCTCCAGGTGCTCCAGGCTTTCCTGGACCTAAAGGTGAACCCGGTGACATCCTCACATTTCCAGGAATGAAGGGTGACAAAGGAGATTTGGGTTCCCCTGGAGCTCCAGGGCTTCCTGGTTTACCTGGCACCCCTGGACAGGATGGATTGCCAGGACTTCCTGGCCCCAAAGGAGAACCT
Seq A exon
GTAAGTTGGCTTGATATTCTTGATTTTGTGGTGTCAAATTGTTAGTGATGTTTTCTAGGATGGGCCTGGTGCTGAGATGAACATCTAATCAATGCTTAAAAGAATGTGATTATATGTACTAATGGCACATTGTTATTGACTATGTAGAGTTTCTTTATAATTCTTTTCTCTAAGTGGTTTTGTTAATTCTTTCTGCTTAACCCACTATTATGTTGAGTACTGTTTGCTATGACCAAATAGGCAGAAGGTTAAGATGCCTGTAGATCAGTGTAAGTTTCCCATTTTCTTATCCTATATAGCCTTGTGTGGTTTTGTTTAGACCTGACAATAAAGGTCTAATTTGGTTTATATACAGTAAGCTTAGAGATTAGTATGAGTAGATGGCTGTGTTAAATGTGCCATGGAGCCTAAAGATTGAACATAAATGAGTAGAGCCTTATTTTGTGCGCAACACACAGCCTAGGATATTTAGGTAGAAAGTGATACTTTATAAAATGTTAACTAGCCTGTAAACTTCTTGACTTAACACTAGAATGTAAGCTTAATGAACATAGAGACTTTAGTCTATTTTTATTCTTTGCTCTATCACCAGTTCCTGGCACATAGTAGGAACTCAAAAAATATTTGTTGAATGAAAGAATGTATAAATAGAGTGATCACACATACCATCCCATAGTAACACACACTCAGTTTTTAAGAAGAACTATTATGGCTGTATCATTTCTCTAGCTGTACTAATACCAACCTACAGATAGCTGTTATATCTATGTATTTCTGTATTAACCTTTTCCCTTTCAG
Seq C2 exon
GGTGGAATGGCTTTTAAGGGTGAAAGAGGTCCCCCTGGGAACCCAGGTTTGCCAGGTCTCCCAGGAAATAGGGGGCCTATGGGCCCTGTTGGTTTTGGTCCTCCTGGTCCAGTAGGTGAAAAAGGCGTACAAGGTGGGGCAGGAAATCCAGGCCAACCAGGAATACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014575:ENSBTAT00000019400:25
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(32.3=32.8),PF0139113=Collagen=PU(70.7=64.1)
A:
NA
C2:
PF0139113=Collagen=PD(25.9=26.3),PF0139113=Collagen=PU(85.0=89.5)
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:
CTCCAGGTGCTCCAGGCTTTC
R:
CTGGTATTCCTGGTTGGCCTG
Band lengths:
348-1146
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]