RnoINT0070921 @ rn6
Intron Retention
Gene
ENSRNOG00000011015 | Hivep2
Description
human immunodeficiency virus type I enhancer binding protein 2 [Source:RGD Symbol;Acc:61988]
Coordinates
chr1:8324650-8326376:+
Coord C1 exon
chr1:8324650-8324751
Coord A exon
chr1:8324752-8325480
Coord C2 exon
chr1:8325481-8326376
Length
729 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGT
5' ss Score
9.73
3' ss Seq
TTACTGTTGGGTTCTTTCAGAAA
3' ss Score
8.67
Exon sequences
Seq C1 exon
GAAACCTAACGAAACACATGAAATCTAAGGCCCACATGAAAAAGTGTCTGGAGCTGGGCGTCTCGATGACATCAGTAGATGAGACAGAAACAGAAGAAGCAG
Seq A exon
GTGCGTGACTTACTGAATGGACTGGCCTCTTAGGCGGACTTTGTGGTCTAGTGATTGCACGTCGCCTTATTAAGTAATCGTTGCAGGAAATAAAACAGCACACTGAACTGCTTGAGAGCTACTAAGGAGAAAGGAAAACATTTGAGTGTAACTTGTTCTAGAGGTGGGGAGGGCTGTGTTAGCAAAATAGTTGTCTCTAAACACTGTGAAGGGATGTGTGCATGAGGCAGGGGATGGAGTTGTGATTTATGTGCTGGGAAGCTTTGGGAGGAAATTGAAAGTATTTTAATGTGTTAGTCTTCCTATTGAGAGGAAATGTAGTAGAAAAAAATATCCATCATTAACCCCAGTAGAGGATCTGAAGGTCGGCAAACCTCCTGAGGGATCCCTCTTACAAATAACTTGCACCTCAACAGGAGAGGTGGGCCATCGCTTTGCTTTTCCTCCTTCAGCATCAGTTATTAGCAATACCAGACACATCCCTTTGTTTTGAGTTGTGTCATGAGACTTCTCTGAAGTCTGAAATATAAAATCCTATTCCAGGGTTCTCAGGGATGAAACCAAGTAGGGTAGGCACAAGTAAGTGTCCATGGGTGGTTGAGAGGCATGATAATTTTAGGGGGTCAAGAGGGTCAAGGAAGGCTTTTGGGAAGATTGTTGGGGCAGATACAAGCTCCTAGCCTTGAAAATGGGATCTTAACTACCGTTGTTACTGTTGGGTTCTTTCAG
Seq C2 exon
AAAATATGGAAGATTTGCACAAAACATCTGAGAAGCACAGCATGTCCGGCATTTCAACTGACCACCAGTTCTCAGATGCTGAGGAATCTGACGGAGAGGATGGAGACGATAATGATGAAGATGATGAAGACGATGATGACTTTGATGACCAAGGAGATTTGACACCCAAAACAAGGTCAAGAAGCACCAGTCCTCAGCCTCCTCGGTTCTCCTCCTTGCCTGTCAATGTTGGCGCTGTAGCCCACGGCGTCCCCTCAGATAGCTCTCTGGGACATTCGTCATTGATCAGCTATTTGGTTACTCTACCCAGTATTCAGGTCACTCAGCTCATGACACCCAGTGACTCTTGTGAAGACACCCAGATGACAGAATATCAGAGGCTGTTCCAGAGCAAAAGCACAGACTCCGAACCCGACAAAGACAGGTTAGACATCCCAAGCTCCATGGACGAAGAGGCCATGTTGTCTTCAGAGCCGAGCTCCTCCCCAAGGGACTTCTCCCCCTCAAGCTACCGGTCCTCACCAGGATATGATTCTTCACCCTGTCGAGATAATTCGCCAAAGAGGTATCTGATACCCAAAGGAGATTTGTCACCCAGAAGACATTTATCACCTAGAAGAGATCTATCACCTATGAGGCATCTGTCACCAAGAAAAGAAGCTGCATTGAGGAGAGAGATGTCCCAAGGGGATGCTTCACCAAGGAGGCATTTGTCCCCACGGAGACCATTGTCTCCTGGAAAAGACATTACAACAAGAAGGGACCTCTCTCCCAGAAGAGAGAGAAGATATATGACTACCATTAGAGCACCATCTCCCAGAAGGGCTTTATACCATAACCCACCATTACCAATGGGGCAGTATCTGCAAACAGAGCCAATTGTATTGGGGCCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011015:ENSRNOT00000015131:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.400 A=NA C2=0.977
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:
AAAAAGTGTCTGGAGCTGGGC
R:
TGACGAATGTCCCAGAGAGCT
Band lengths:
345-1074
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]