BtaINT0065481 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011544 | GAPVD1
Description
Bos taurus GTPase activating protein and VPS9 domains 1 (GAPVD1), mRNA. [Source:RefSeq mRNA;Acc:NM_001102520]
Coordinates
chr11:96170237-96172896:+
Coord C1 exon
chr11:96170237-96171080
Coord A exon
chr11:96171081-96172809
Coord C2 exon
chr11:96172810-96172896
Length
1729 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
ACCTCTGTTCTGGGTTGCAGGTT
3' ss Score
10.17
Exon sequences
Seq C1 exon
TGCTGAAGCTTCCCCTGCTGAATGTTGCCAACATGCTAAGATTTTGGAAGACACACAGTTTGTTGATGGGTATAAGCAACTGGGATTTCAGGAGACTGCTTATGGAGAATTCTTGAGTCGACTAAGGGAAAATCCTCGTCTTATTGCCTCCTCCTTGGTTGCTGGAGAGAAACTTAATCAGGAGAACACACAGAGTGTCATTTACACAGTTTTTACCTCTCTCTATGGCAACTGCATTATGCAAGAAGATGAAAGCTACCTCCTTCAGGTGTTGAGATACTTGATTGAATTTGAACTTAAAGAAAGTGACAACCCCAGACGACTTTTGAGGAGAGGAACCTGTGCCTTCAGCATCTTATTTAAACTTTTTTCTGAAGGACTGTTTTCTGCCAAACTTTTCCTCACAGCTACTTTACATGAGCCGATCATGCAACTGCTTGTTGAAGACGAAGATCACCTGGAGACAGACCCAAACAAGCTGATTGAAAGGTTCTCCCCAGCTCAACAGGAAAAACTCTTTGGAGAGAAAGGCTCAGACAGGTTTAGGCAGAAGGTTCAAGAGATGGTGGATTCCAATGAGGCCAAACTTGTGGCCTTGGTGAACAAATTTATTGGTTATCTCAAACAGAACACTTACTGCTTCCCACATAGTCTGAGGTGGATTGTGTCACAGATGTACAAAACTCTCTCCTGTGTAGACAGACTGGAAGTTGGGGAGGTCAGGGCCATGTGCACTGACCTCCTGTTGGCCTGCTTCATTTGTCCTGCAGTCGTCAATCCAGAACAGTATGGAATAATCTCCGACGCTCCCATTAATGAGGTGGCGAGATTTAACCTGATGCAG
Seq A exon
GTATGCTTTTCCTGGGCATTCAGTGTGAAACCAGTTGATTGGGCATTGGGGTGGGAACGGAAAGTATGATGACATTGTTCGTATATTCTTAACATTCTTTTCCCCAAAGTGTCCCAAATATTTGCTTCTTAAGTTTTGTGTTCATTTTTAAATGGAGTCCTCACACACTTTAAATATTTAGATGATTCCATTTTCTAGAACAAGGCCACCATCCCTTTCCCATGATTTCACAATTCAGAATGATTAAAAACTGAGGTGGTCTTTTATACTTCCTTTGGTAGCAAAACCTATCCTGAACTAACAAGAGGCTGTTTATAGTCCATTTCGTGTTAATGAGTATTTGTGTTTTGCTGCGGGAATGTTAATGTATCTGATTATAGGATGCCACCCTAAATACTGGGCATGTTACGTATGTATGTTACCAGCCTTTCTAAAATCTCCAGATTTTGAAATCTGAAACTCTTCTGGACCTAAACGTTTTCAAAAGAAGATTTTTGGATCTATGTTAGCACTTTTTTCCCCCCTAATCATCTAAACTACTGAAATCATGTTTTTATTTCTTAAGGGATTCTTTTAATTATATGTTATTCCCAAAAATACTGTGAAGAAGATAGAGTTTATTTGGAATACCATATATCTTATCTTTGGATGATTATTTTTTTAATGATAAGCTTTTTTTTCATGATTAGTTCTGTCATTTTGGGGTGTTTAGAAATTACATAGACATCCCTAAAATAAAATTAGAATTTCTTTGTCATCTCTGAAACACTAAATTTATTCTTACGATAACATCATTATAGTTTTATTTTTGTCATTCCAGTAGAGATAGAATCACATGCTTTCAAAATGAGTAAAAAGAGGGATTGTCCCAGATTTGAAGATGATGCTATATGATAACTTTCAGCAAAATATCTTTAGAGAGTAGATTAACAGTTCACTTTTTGCAGTAAGGATCTGGCTCTGAGAGTTAATATTTACTTTCAAAACAGCTTATGCTCTGTAGGAATTATTTGCTTTCAAGTCTAGAAAAAATGTTTTACCTTGAGTACTTTATGAACTATAGAAAAAAGTACTTAATAATAACTTGAGATAGTTTGTCAGCTTTTACAAATTAAGTTTTTAAAGATACGGTAAGTACAGCAGCAGAAACAAAGATCATGTACCTTCATTTCCTATTGTCGATATAATATGCATTAAAGACAAAGCAAAATTTTCTACTTATTCATTATAGCTCAGTATAAACATAATAAAATACAGTGGGCTTCCCTGGTGGCTCAGTGGTAAAGAATCTGCCTGCCAGTGTAGGAGACACGGGTTTGATCCCTGGTCTGGGAAGATCCCACTTGCTGGGAAGCAGCTGGATGCGTGCACCTCAACTACTGAGCCCTTGCACTCTAGAGCCTGTGCTCTGCCTCCAGAGAAGCCACCGCACTGCAACTCAAGAGAAGCCTCGGCTCATTGCAACTAGCGAAAAAGCCTGTGCGGCAATGAAGACGCAGTCTAGCCAAAAATAAATAAATAAATAAAAATGTAAAAAACAGAAGTCCTTAAAATATAGTAAAAGCTGACAGAGTCAAGATGCATATTTTATTGGGGATCCCATTTTGTATGCTTGGTTAGGTGATGTGAATATTCTTATGAAACAGATTTTTAGAGTAGAATGGAGATGGTTTCACAGTGGGGACTGTCTCTCCAGCCTGCGTCTTCCCACCTCTGTTCTGGGTTGCAG
Seq C2 exon
GTTGGCCGCCTTTTGCAGCAATTAGCAATGACTGGCTCTGAAGAGGGAGATCCCCGGACAAAGAGCAGCCTTGGAAAATTTGACAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011544:ENSBTAT00000015341:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.138
Domain overlap (PFAM):
C1:
PF0061614=RasGAP=PU(94.6=67.7)
A:
NA
C2:
PF0061614=RasGAP=PD(4.5=31.0)
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:
AGGCTCAGACAGGTTTAGGCA
R:
TGCTAATTGCTGCAAAAGGCG
Band lengths:
343-2072
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development