BtaINT0041869 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014575 | COL4A5
Description
collagen, type IV, alpha 5 [Source:HGNC Symbol;Acc:HGNC:2207]
Coordinates
chrX:61751308-61753532:+
Coord C1 exon
chrX:61751308-61751476
Coord A exon
chrX:61751477-61753439
Coord C2 exon
chrX:61753440-61753532
Length
1963 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CACTATTAATTCCCACATAGGTC
3' ss Score
6.34
Exon sequences
Seq C1 exon
GGTGGAATGGCTTTTAAGGGTGAAAGAGGTCCCCCTGGGAACCCAGGTTTGCCAGGTCTCCCAGGAAATAGGGGGCCTATGGGCCCTGTTGGTTTTGGTCCTCCTGGTCCAGTAGGTGAAAAAGGCGTACAAGGTGGGGCAGGAAATCCAGGCCAACCAGGAATACCAG
Seq A exon
GTGAGTTTGCTATGGCTGTTTCATTTTTAGTTTGGTGCTTACAAACAGAAATGCATTATCTTTTGACCATTTTGGGTTCCTTTCATGAGAGGTGTTTTTCCCTGGCTATTTATATTTGGGCTTTCCAGAGCTCCTTAGCAAGGAAACACAAATGCGTATGTGCATGTGTGTGCATGTGTGTGTATGTTTTAAGAATGCCTTCTCTTTAAAGTTTCTCTGACTGTATTTATTGTTCCTGTTGTTGTTTTTAAGTGCATCATACGTAATGCAAAGTTTAACAAATAATTATAATCGAAACACACGCGTAACTACCACATGTGCCAAGAAATATACATTGCCAGTATTCTGGAAACCTATGCTCCCCTCTCTGTCTTTTCCTGTTAAAAATCTTCTTCCATTTCTCCAGAGGTAAACACTGCCTTCACTTTTGCATAATTTTCTTCCATAAATAGTTTTATCACCTAGATATATATTCCTAAATAAAGTACTTTATGCTTCTTTTTGAACTTTATGTTAATCATAGGGTAAGTATTCTTTATGTTACCTTTGTATATGGATATAGCATTTTTATTGCTGTACAGTGTCCCACTGTGTGTGTGTCACCATTGATTTATGCATTCTATTGTTAATGGACAATTGGATTATTTATTGTTCGGGCCTGGTATTATAATGCTTCTATGTGCATTCTCTTATATATTCTTGTGCTCTGTGGCAAGGATCAGCAAACTACAGTTCATAAATCAAATCTGACCCTCCACATGTTGTCATAAATGAAAGTTTTATTTGAACAGATTCCCACCCATTCGCTATTGTTATGCTTGCTTTTGCACTACTGCTGCAGAGGTAAGTTGTTGCCACAGAGACCGTGTATGGCCCACAAAGCCTAAAGTATATGCTGTCTAGTCCTTTACAGAAAACAATTGCCAGTAACTGGGTTAGGGTATATATTTAAGATTTGCATTTTTGAGGCACAGAATAAATACATCTTCAGTTTTACCAGATAATTCCAAACCATGTCCAAAGCAGTTGTATCAATTCATACTCCCACCAGCAGTATTAGAAATTTATTGTTGGTCTGTATCTTCAAAAACATTTTGTATTGCTGCTTTTACACTTTTGCCAGTCTGTTGAGTGTGATATATAGGGTGGCAGATTTATTTTATATTTCTCTGATATATAAATGAATAAAAATGAATATGCAATATCCATACACAAAGTTAACATGAAGAATACTTACCCCATGATTCCATTAACATAAAGTTCAAACATTAATATTTTCATATGTTTGTTGACCATTTGAATTTTCCATTTGTGACATTTCTATTCAAGTGTTTTGACCATTTTTTCTTTGGGATTGTTTTTCTTACTGATTTGGAGGGGGGTGTGTGTGTGTGTGGATTCTGTGTATTAGTTCTTTCTTAGCTATTTATTTTGCAAAATTTTCATTCACTGTGACTTGCCCTTTTCACTCTCTTTATGGTGTCTTTAATGAACAGAAATCAATTTGAGTGTAGCCAAATTTATCAGTCTTTTCTCTCATGGTTAGTGCTTTTTATGCCATGATTAAGAAATCCATCTTTATCCTCAACCTTTTTCAAAGTCTTATTTCAATTAATGAGTAGTATGTGTACTTGGACTTTGCACACATAAAACCTTAAAGTACCAGTAGTTAACCAAAAAGAAATATTTTTCTTTTGAGCTGCATTTAGAAAATATTTTTACAGATGCCTAATATTTTTATAGATGCTATCTTCATGAAAATTCTTAAAACTGTAATATACTTTTCTCTTTGAAATTTCATTCTTCTGTTTAGTATCTTCCTTGAAAATATATATAAGATTGTTTTTCTCTTGAATTTTTATTAGTTTGCATTTTCAAAAGATTATAAATATTTTTTTTGTTTTAATTAATGGAGGTCTTTAGTCAAGTGAACACTTCCTATTCACTATTAATTCCCACATAG
Seq C2 exon
GTCCTAAAGGTGATCCAGGTCAGACCATAACCCAACCAGGGAAGCCTGGCCTGCCTGGTCACCCAGGCAGAGACGGTGAAGTAGGTCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014575:ENSBTAT00000019400:26
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(25.9=26.3),PF0139113=Collagen=PU(85.0=89.5)
A:
NA
C2:
PF0139113=Collagen=PD(13.3=25.0),PF0139113=Collagen=PU(44.9=68.8)
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:
GGTGGAATGGCTTTTAAGGGTGA
R:
CCTACTTCACCGTCTCTGCCT
Band lengths:
254-2217
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]