BtaINT0065479 @ 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
chr11:96205562-96207009:+
Coord C1 exon
chr11:96205562-96205634
Coord A exon
chr11:96205635-96206811
Coord C2 exon
chr11:96206812-96207009
Length
1177 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATA
5' ss Score
7.96
3' ss Seq
CTGTGTGTGGTCTCGCTTAGGTT
3' ss Score
8.76
Exon sequences
Seq C1 exon
GGTTCTTCATGAACATATTCAGAGATTGTCTAAAGTAGTGACTGCAAATCACAGAGCTCTGCAGATACCAGAG
Seq A exon
GTAATAACAGTTTATACAGTATGGATGGTATTATTCAATTAAAAGTGTCTTGGTGTGCTATGTACATGTTACCAATTTTTCAGGGAAGCAGAATATAGTAAGTTATAAAGAAACCACTTGCACTGGATGTCCTTCAGCCAATAAAATTCTCAAAGGTCTTTCCGTGGATTAAAATTCCCTAGCCTGAGAAAGGACCTTAGTAGTGAGAGGTGAGTGGAGGGCCAGCCTGGGGTAGCCCCCGCCCTGACATCACCCCCTGTAGGCAGGGCTTCCTGCTCACAGCTCACTCCTCCTGCGGCAACCACACACTCCACTGATGCTTTTATTATCATATAGAGCCTTGGAGTCCTAACCACTCAATAGCCAGTGTTCTTTCCAGAACATTCTGCAGGAATGTCCCATATGAAAGGATCTGGTGGAACTTCAAAGAGAGTGTGGAAACTCCTGTCCAGAAGAGGGAACTGAATCTGAATGTGACCTCAGAATTACCTTTTAGTTCCTAATAGTACATTTTTACCTGTCTTACACCTCTTACAAAATCAGGAAACAGGAAAGTTTTAGGTATATGAGTTTTCTGGTTGTTTCATTAGAATCTGGATATTAATTGGCATAAAATTTTTAATTGTCCTTGATTTCTAGAGCTGCTGCAACACAGGTACATACTAATTTTTAAGCTATTGTAAAAGTAGCTTGTCGGTGCTTTTGGAATCAGCTGCAATACATAGATAAGTCCCATTCTAGCTCTTTTAAGAAAGATAATTGTTTTAAATTTATGAATTCTAGGTTCTGTGTTATCAGATGCCTCTATTACTATATTTCTGGGTGGGTTTGTGTGTTTGTTTGTTTTTCCTTTGGGGCCGCATCATGCAGCTTGGGGATCTTAGTTCCCCAGTGACCGGGGATGGAACCTGGGGCCCTGGCAGTGAGAGCTCAGAGTCCTAACTACTCAACGGCCAGGGCATTTCTCTGGGTGGTTTTATTTTAAAATTCAAAGCAAATAATTTAAAAGCTTAAAAGTTAGGCTTCAATCCTGAAGTGGGAGGATGGGGAGGAATTGCAATTTGGTTTTTCTGAAAAAGGGAAAAGGCAGCGGCTTCACCCATCCGCCTCCTGACGTAGAGGTTGCTCTGGTCACTGCTTCCCACGTGCATGACAGTCTGTGTGTGGTCTCGCTTAG
Seq C2 exon
GTTTATCTTAAGGAGGCACCGTGGCCCTCGGCACAGTCAGAAATCAGGACAATAAGTGCTTACAAGACGCCCCGGGACAAAGTGCAGTGCATCCTGAGAATGTGCTCCACGATCATGAACCTCCTGAGCCTGGCCAACGAGGACTCCGTCCCAGGGGCAGATGACTTCGTCCCTGTGCTGGTGTTTGTGTTGATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011544:ENSBTAT00000015341:23
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0220413=VPS9=PU(56.3=87.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCAGAGATTGTCTAAAGTAGTGACT
R:
CTTGATCAACACAAACACCAGCA
Band lengths:
254-1431
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development