BtaINT0065487 @ 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
chr11:96178660-96180708:+
Coord C1 exon
chr11:96178660-96178785
Coord A exon
chr11:96178786-96180534
Coord C2 exon
chr11:96180535-96180708
Length
1749 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
CTTAATTTTGCTTTTGCTAGCTA
3' ss Score
4.46
Exon sequences
Seq C1 exon
GTCCTTCAAATCGTTCTAATTCAGTGTCCTCACTAGACCTGGAGGGGGAATCTGTGTCAGAGCTTGGAGCAGGACCTTCTGGGAGTAATGGAGTTGAAGCTCTACAGCTGTTAGAGCATGAGCAAG
Seq A exon
GTAAAGTGAGGTTGAATTCAGTTGCTCAAGTAGCAGAGAATTTACCTGGTCACAGAATAAGCAATCTGTTTTCCTGTGAGTTGGCTGTGTTCAGTTGATTATATAATGACCATTAAACTGGCATTTATTCATAGTTCCTACATTTCTTAAAAATGTGTTTGGTTGGGAATTCCCTGGCAGCCCAGCAGTTAGGACTTGGCACTTTCACTGTGATGGCCTGCTTTAATCCCTGGTCGGGGAACTCAGATCCTGTAAGCTGCATGGTGGAGTCAGAAAAAAAAAAGTGTTTAGTTGCTAAGTGGATTATTTAGGCTTAAATTACATAGAAGAACTAAAATGAATTGCTTGAATTGTGTGATACTTGGTATTTCAGTTCTGTAGTATTACAATTTTAAGCGGTGCTAAGATAAATTCTGAGGGCTCAAGGAACTTAGAATAGGGAGAAAATGGTACGCAAATGATTAAAATGATCATAAAAGTGCATTGGCAGTTCTGGGTAAGAAATACATGTGGTTCAAAGTGTAGGGAAAAGCTTATAGGGAGAAAATACTAGCCTTGAAGCCTGGCTGGCATTGGCATTGGCTGAAACTAGAGATACTCTAGGTAAAGTAATATTAATAGTATAAGCAAGCTGGGAAACCATAGTACTCTCTCAGGAACTGTCAAGTAGGGTGATAATGTGAGGTTAGGATGAAAAGCAGATGGATCCCTGTTGTCCTTGTAGAAAAAGATCACTGGTGGATTTTATGGGAATGTTTATTGCCCTCAACTGGATTTGAGGCAATGACTTCAGTGGGTGTAAAAATCACCTGAGGAGTTAGGAAAAAAGGAAAAAAAAAGAAAAGGCATTTCCCATGTCTCATTTCTAGAAATCATGGTTTCATCTCTTTTTAGAAGGGAAAAGAGGGTTGCCAGTCAGGTTACATGTGGGTTGAATAAAAGTAAGGCTGAGTTTTACTGAATCAGTTTGTCACTGTGTTATTTAGGATTAAATTTTCTGCAAAAAGCAGAAACCTAAAATAATATTAGCTTAAGATGGAAGTTGAAAGAATATCACTTCTTTAACAAACCTTTTAGGTGATTCTGGTATTCTTTTTAAAAAATATTTATTTGGCTATGCCAGGTCTTGGTTGCAGCACGAAGGACCCTTAGTTACAGCTTGTGGGATGCAGTTCCCTGATCGAATCTGGACCCTCATGCATCTTGGATCACTTGTAGTCAAAGTAGGGAGCTCTGCTAATTTTAGCTGGGCGTCTATTGGTCAGTGGGGAGCTGGCTAGTCTAGGATGACCTTTCCTTTGTTCCGTGTGGTTCCTGCTCCCCTAAAAAGCTGGTTTCAGCTTGTCCTCGGGGCAGAAGCAAGGATGAGAGAGAGCAGATGCTTGTGAGATCTCTTGAAGCCTAACCTCGCAACTGGCTCACTTCCTCTTTATCCTTTCAGACAGAGCAAGTTACCAGGCCCGTCCAAATTCGAAGAAGGGGGCATATATCCCAATTCTTGAACAGTGTCACACTACTGAGGACGTGGAGACAGTAACTGACCAGAAGGGGGAGGACATATGTTGAGCTTGGTTCAGAGAGGGAAAGAGTACATCCATGAGGGAATAATTCCGTGTTTTGGTACTGTGTGCTGAATGTTCGTGTTCAAATACATAACTTGGAGTTCAAACACATAAAGTTCTTTAAAGTTGATTTTAAAAATGGTAGCTATGCTGTGAGTTTTAAAGTGCTTAATTTTGCTTTTGCTAG
Seq C2 exon
CTACCACGCAGGATAATCTTGATGATAAGCTCCGGAAGTTTGAAATCCGTGACATGATGGGACTGACGGATGACAGGGATATATCAGAAACAGTGAGTGAGACGTGGAGTACGGATGTCTTGGGAAGTGATTTTGACCCTAACATTGACGAAGATCGCTTGCAAGAAATCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011544:ENSBTAT00000015341:9
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=0.949
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CAAATCGTTCTAATTCAGTGTCCTCA
R:
CTGCGATTTCTTGCAAGCGAT
Band lengths:
294-2043
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development