RnoINT0063981 @ rn6
Intron Retention
Gene
ENSRNOG00000017925 | Gapvd1
Description
GTPase activating protein and VPS9 domains 1 [Source:RGD Symbol;Acc:1307479]
Coordinates
chr3:13786183-13788135:-
Coord C1 exon
chr3:13788006-13788135
Coord A exon
chr3:13786309-13788005
Coord C2 exon
chr3:13786183-13786308
Length
1697 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAG
5' ss Score
5.73
3' ss Seq
CAGGATAAACATTTTTCTAGGTC
3' ss Score
4.6
Exon sequences
Seq C1 exon
GTTCTAAACATGCAGCTTTCGGACGGAGGACAAGGAGATGTCCCTGTTGATGAAAACAAACTCCACGGTAAACCTGATAAAACCTTGCGCTTTTCCCTGTGCAGTGATAATCTGGAAGGCATATCTGAAG
Seq A exon
GTGAAGGGTTACTTCATTCAGGGAGTGTGTGATTGAATTGTTCTGTGTTCTTTAAAGGAGCCTTATAAATTATAGTTAAGCTACCTGTGCCCCTCACTAAGGAGGATAGTGACATTTCCTCTAATGAACTTTAACGTGGCTGTGAGATTGTTTCCTAAGTAAAATTAAGATTGCAAGAGGCTGTTGGCCATAAAATGACAAGACATGTCTTCACTCTGTTAATAACAGCAGGCTGTGTTTCTCAGTCTTAATGCCTGCACAAGCTTATAGCGCTCCTTTAGAAGGCTGTAGTGCATGTCTAATGGGGAGAATGGACTTGCTGGTATTTCAGGATGTTGTGTATACGTTTTCACTGTTCTGTGTTCTTTATCCACACACCCACACATGTCTCTATGAATCAGGACACTGTGGAATAAAAAAGGCAGGCAAGGGTGGGATGCAGTTGGTAGAATGTTTGCCTGGCATCCCTAGACCTAATCTTCTGTAGGTGGGGAAAAAAGGAAATGGAAACTCTTAAACCAGATTGTGAAGTTAAGAGTTTGTCATTCCATGTATTAGGATAGTTTGTTTTATGAAAAAGTTCAAGTTTACTAACATTTAAAAGAAGACATAAATATTCTCTTTAACCTTTCAGAAAAATCAATGAGTAATATATGTTTAATCTAGAAAATGTAGAAAAGATTATTTATAGCAAAATCAAGTTTATGGTGTTTTATAACCTTTTTATGTCATGTGTCATTAACATTCCCTTTGTATTTTGCATTTTAAAATGACAAACTTTTATTTTTATGTTTTTTTCTTTCCTTATTTTGAGACAAGGTGTTACTGTGCAGCCCTGACTGAGCCAGAATTAGCTATGCAGATCAGACCTGACTTGTACTCAGCAAGAGATCTTCCTACCTCTGTTTCCCAAGCGCTAGGATTAAAGGTGTGGCCACCATGCCTGGCAATTTCATCATCTGAGTGACAGAGGCAGGTGAATCTCTGAGTTGGAGGACAGCTTGTCTATAGACTGAGTTCCAGGACAGTCAAGGTTACACAGAGAAGAAACCATGTCTCAAAAAAAAAAAAAAAAAACCAAGACAAACAAAGGAATTGTCTGATTTGCTTGCCCTGTCATTGGCTCATAGATGGTTTTAAACTGGCCATTAAACCTTGTCAACCTTGGCTGTGTTCATCTGGATGGACATACGGCCCTTGGCAATAATGATTGGGTCATTTGCAGAACATTTCCAAGGGGTGTGCAGGTCCATGAACCTGCTGGCGTTCTGCGTGTCTAGGCACTGCCTGGTCACTCCTGCTGCACGCACACACAGAAAGCACTTCTGACTTTTACGTATTATAATAGTTCTTCAACAAGCAACTTTAGGTTATTTTTCCTATAATTTTTTAAAGATAAATTTTTAGAGATAGAGCTATTGGCTCAAAGGCATCTATATTTTTAAGGAAATAAATACACTATTAAAAACATCTTAAATCTGGCATGATGACATATATCTGTAATTGCGGGGTTCAGAATGCTGAGGTAGAGAACTTGAGAGTGTAAGATTAGTCTGGGTGATATAGTGAGACCTTTTTTCAAATCAGAACAGAACAAAACCAGAACAGAAATAAACACTATTTTCATGGCATGAAATATTTTATGTTGACTTATGAATTTTTAAAGAAGATTGCTGACAGGATAAACATTTTTCTAG
Seq C2 exon
GTCCTTCCAATCGCTCTAATTCAGTGTCTTCTCTCGACCTGGAAGGAGAGTCTGTATCTGAACTTGGGGCAGGACCTTCTGGGAGTAATGGAGTTGAAGCACTGCAACTGTTAGAACACGAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017925:ENSRNOT00000066961:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.864 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCTAAACATGCAGCTTTCGGAC
R:
TGCTCGTGTTCTAACAGTTGCA
Band lengths:
254-1951
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]