DreINT0078045 @ danRer10
Intron Retention
Gene
ENSDARG00000075928 | hivep3a
Description
human immunodeficiency virus type I enhancer binding protein 3a [Source:ZFIN;Acc:ZDB-GENE-081029-2]
Coordinates
chr19:15408159-15410196:-
Coord C1 exon
chr19:15410095-15410196
Coord A exon
chr19:15408830-15410094
Coord C2 exon
chr19:15408159-15408829
Length
1265 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
GTGACTCTTTTGTGCTGTAGGTG
3' ss Score
9.21
Exon sequences
Seq C1 exon
GGAATCTAACCAAACATATGAAGTCAAAGGCTCATGGGAAGAGATGTCCAGAGGGACCTGCTCCAGGACCAGTCCAGTGTGAGCTGGAGACAGATGAAGGAG
Seq A exon
GTGAGAAAAAAGTGAGAAAAAAAGTGCTGTATTTTGATGTCAAGTTATGAAGATAAGGATGAAAAAATAAAGAAGAAAAAATAATCAATAAATATTTTAAAAAATGTAATAAATAAAATGTAACTTATGTTTGTTATACATTAATTAAAGACTTTAAAAAATAGAGACCGCTTATTTTTAAATTTTAACATTTTAATTTTGTAGACTACAGATGACATTTCTTGCTAACTAAAATAATAATGTCATTAAGAGCATTGTTTTGGTGCATAAAATAACAAAATGGCAGCATGTTTATGCAAATTTTTAGGTGTTACAATACCAATTTTTTAAAATCTGGTATTAAAGATTGTACTTGGTTTCTTATTGTGATAAAGATAAGTAAAACAGCTTCTCAAATGTGAAAAAAAATGATAAAAGTTGGGATTTGATTCAGTCTTTAAAGAATTTATTGTACGGTTGGGGTATGCTGAGCTATTTAATTAAAGACTACAAAAGCACATTATTTTTCCAAATAATGCATGGCAACGGTAAATAATTTATACTTTTTTCTACAATATTCCACATAAAAATAAAAACTGTAAATTTAGATTTTATAGTACCAAGTTCAGAAGATTAAAAAATATATAGTTGGTGGAAAAACTCAGTTTTATCCAAAATTTTGAGGAAAAAACATTATCAGTGCTTCATTCAAATATAAAATGCCATATATAATGATATATAAAGGATAAAGTACATCTAGTGGCTTGTTATAACAAAAGTTATAGGCTTATCAGCAGCTCAATGCAAAACAGAGGGCTTCATCATCTACATATACTTTATCCTACTGAATACACTGCTACTTGTACAAAATGTAAAAAAAAATTATACAGAACAATTTCTGAGTCGCAGTAGTTTATTAATTTCATAACTAAAGCTAAAGCTGACAGAAATAAAAATGGCTGAATGAAGCATGCACTAACCTTTGTTTTATTCAGTCACAAAATGTCACCAAACAGTACCGTGACAGACAAGCATGTTAATATGGACACAGATGCATTCACTGCACAGTCAAGATGATTCAAAGTTCACAGGATGAGCCTGTGTTCTTAGTTTTGATGGTTGTTATCTGGGAATAACATACCTAGGAATGTTGTGGCTGACCGATCAGATTCAAGTATTCCACACAGCCTTTAATAATGCAAAATAATATATGTATTTGTTGTTTTAAAAATATATTGTATATAATTTCTGTGGAATGCTGATTCTGTGACTCTTTTGTGCTGTAG
Seq C2 exon
GTGACAGTGCTAAACATTTCCTTGAGACAGAGGAAGTGGAAGAACACCAGTTCTCGGATGCGGAAGAGTCCGATGACGAAGCTGAGGATAATGATGAAGGTGACGAGCAGACTTCATGCTCCTCTTCGTCATCCAAGTGGACGTCCATCTCCAGAGATGATTCTGGCTCGTGTGACATCTTAGGCCTTTCAAACCCAGGCTGGGAACAGCATCCCAAACCGCCTGTCAGTATGAGCCCTCGAAAGCCCAGCCACTATGGAGAAGCTTCCTCTCCGAAGACAACAAAGTCTATAGTGACACTTTTGCACCTTGATCCCACCACAGGAATGTGCTCATCCCCAATCCGTAGCCTTTCTCCTGGCCTGCAAATGTCCCCTGCTTTACCACAGTCTCCTGGACGGGACATGTCCCCTCTACGATGTCCTTCTCCAAGACTAAGTCTGTCTCCATCATCCTGTCTGTCCTCATTGTCTCCTTCTGACCGCTCGACTTCATCCTTCTCCGAGAGACGTGTGTCCCCCATTAGAGACCTGTCCCCCATACGGCCTTCGTCTCCCAGTTGTCCCCTGGCGTTGACTGTTGGGGCCAGTGTAACTATTCAGTACCAAGCTGACAGACCCAGAGCTTCAACAAAAGCCTCACCTAACAGGTTAAACCTCAAGAAAAAAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075928:ENSDART00000143480:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.800 A=NA C2=0.875
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:
TGGGAAGAGATGTCCAGAGGG
R:
TGTTGTCTTCGGAGAGGAAGC
Band lengths:
352-1617
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]