DreINT0071423 @ danRer10
Intron Retention
Gene
ENSDARG00000090183 | gapvd1
Description
GTPase activating protein and VPS9 domains 1 [Source:ZFIN;Acc:ZDB-GENE-040718-117]
Coordinates
chr8:34433996-34436071:-
Coord C1 exon
chr8:34435940-34436071
Coord A exon
chr8:34434126-34435939
Coord C2 exon
chr8:34433996-34434125
Length
1814 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGT
5' ss Score
7.81
3' ss Seq
TGATTTACTTTGTTTTTCAGAGT
3' ss Score
9.72
Exon sequences
Seq C1 exon
ATGAGCCTTCACTGCTCAGACAGAGCTCCAAAACCCAGTCAGCAGAGGCAATTATGGACAAGTACATCAGGTACATGGAGAAACGACCCGCACAGGCTGACGGAGCAACTGCTGGAGGTTATGTTGGACAAG
Seq A exon
GTTTGTCAGAATAAAACACAACACACGCTCACCCAAAAAACAAGTGAGCAGTATTCTTCCTTATATTCAGTGTTGTGCAGGGTGTCCACGTAGTCTTAAAGTCTTAAATAAAAAAAAATTAGGGCTTAAAAAGTCTTAAACTCACTGAAATATTGACTTGAAGTTCTTAAACATTTTAAATGGGTCTTAATTTTTCATTGTCCATGTAAAGCTACCCAATCAGGCCAACACCCATACAGTCACCAGCAATACATCTCAGTAAAACTTTTAACAAAACTCTGTTTTGTTGATTTGGTTACTCACAATAACATTTGTAAGCTCTCCATGTGTTTATAGACCATATGTGGTGGGGACACTGACCTGGACAGACTGTTGTACATTTAGTTTATGATAGTTTTTAAAACTCGTCAAAGAATGGGGAAAAAGTGTAACTGTCAATATGGTGAATGAAGCCCCGCCTACTAGCACAGGATCAGCACAGTGCACTGCCGATCAGCAGTCGCTAAATGGTGAATAAAGCCCGCCTTTTAGTACAGGAGCCAATTAACGATTGCTTTAGAATGACAATTCTTCTGGTGAGGGGCTCTGACCAGATGTAAGTTTTTAAAGATTTTGGTGATACAAACATTTAGAAATGAAACTAAATAGACAGTTGTTGTTTAGTTTTATTGGTTATTCGTATTATGAAATGTAATGGTAAGCTTGGCAAGTATTTTTGGAGAATTTGATGTTTCCCCATTCAAGCAGAATGCTCAAGCATACTGCCCGAGAGGCATTTTAAAGATGGCTGCCGAGTGAAATGACTTGCCTTAAAGCAAAGTGTCCAAACTCGGTCCTGGAGGGCCGGTGTCCTGCATATTTTAGTTCCAACCCCAATTAAACCGTCTGAACCAGCTAATCAAGCTCTTTCTAGGAGTGCTAGAAACTTCCAGACAGGTGTGTTAAAGTAAGTTAGAGCTAAACTGAGCAGGACACCGGCCCTCCAGGAAAGAGTTTGGACACCCCTGCCTTAAAGCCTCAAGTAATTAGAATTTTTTTAATAGGACAAAAAAAAATTCTTATGGTTTAACCATGTCTGAAATTTAACTCAAAACGCTCTTAAAAAGCCTTAAATATGATTTTGTGAAACCTACAGAAACCCTGTTGGAGATGAAATAGAATATTTTCTGGAATATAAGCTGTGGCTAAAGCAGTGGGTGTAATAAAGCAAGAGAAACATGACACTTATCCAAAGGCATTTGTACAAGTTGCTTTTTCTTTTATAAAGTGCTTTTCCCACTCACCAACAGACTTTCATAATAAATGCCGTTTTAAGTCCACTTAAATTTCTGGGTGTTTTCTTTTCTCAACTTTTCTTTTTCTCAATACTTTTAAGAGTTTGTTTTAAAGGGAGGGGAAATATTTAAGGCCACTGGTGGATGTTGCATGAAATTAAACAAGAAGATACAATATCTTTTTTTTAACAAATTTATCATCTAGAAGTATGAGAGTAAGGAAATAAAGCAAATGTGTTTGAGCAGAAGCGATCTCATCGGTCAGTAAAGACTGTTATATCGCATCAGTGTTGCTTTATGTTAAGTGTCTGTTTCATTTGCTTGCATTAATATTGGCTTGTAGGAAAGATTGATTTATTTACTGATTTATGGTAGAGTTTGGGTTTGCATTTTAATTAACTGCATAAAACTGCTTCAACTGATAAATTACTGAAATGTTTTTTTTTTTTTTTTGCCCAACACTGCTTATTTTTCTCTATACTCTCATTCTGATCAAAGTGATCAGTAGTTTGTTATGCACTGATTTACTTTGTTTTTCAG
Seq C2 exon
AGTCTTGTCGAGAAGGGGACAGTGAGCACGACTCTCCTAAAGATGAAGCTCTGCAGAACATCTCTGCTGATGATCTTCCGGATTCTGCCAGTCAGACGGCACCACCTCAGGACAAGACTTTCTCCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000090183:ENSDART00000161282:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.961 A=NA C2=0.955
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCTTCACTGCTCAGACAGA
R:
GGAGAAAGTCTTGTCCTGAGGTG
Band lengths:
254-2068
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]