RnoINT0000178 @ rn6
Intron Retention
Gene
ENSRNOG00000056694 | AABR07001100.1
Description
NA
Coordinates
chr1:37988255-37990007:-
Coord C1 exon
chr1:37989875-37990007
Coord A exon
chr1:37988437-37989874
Coord C2 exon
chr1:37988255-37988436
Length
1438 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
TTCCCTCTCTCCACAAGCAGGAC
3' ss Score
8.13
Exon sequences
Seq C1 exon
TTTCAGGAAATGTTGTCATTCAGGGATGTGGCCATTGATTTCTCTGCAGAGGAGTACGAATGCCTGGACCCTGCTCAGTGGAAATTGTACAGGGATGTGATGCTAGAGAATTACAGCAACCTTGTGTTCCTGG
Seq A exon
GTGAGGAGGATACTTCTATGAAGAACTCTTTTTTTTTTTTTAATTCATCATTCCATTCATTTACATCTCAAATAATATTCTCTTTCCTGGTTACCCCTCCACAACCCCCTCCCATCCCATCCGCCCTCTTCTCCCTTCCCTTTGCCTCTATGAGGGTGCTCCCCTGCCCACCCACCCAATCCCACCCCACCACTCTAGCATCCCCCTACACTGGGGCATCAAGCATCCCTTCCCTCTCATTGATGTCAGATAAAGCATTCTATGCTACTTCTGTATCTGGAGCTATGGATCCAACACTCCTTGGTCTAATCCCTGGCAGCTCTGAGTAGTCCAACCAGCTGATATTATTCTTCATATGGGGTTGCAGTCCACCTCTGCTCCACCAGCCCTTCCCCCATCTCCGCCCCATCAGGCTCCCCAAGCTCAGTCTGATGGTTGGGTCTGAGTATCTGCATTGGTCAGTTGCTGGCAGAACCTGCCAAGGAACAGCCACAACAGGTTCCTGTCATCAAATGTCTTTTGGCAACAGTGTTGGGTTTGGTGTCTTCAAAAGGGATAGATCCCCAGATGTGGGGGTCCCTGGATGGCCCCTCCTTTATCTCTGCTCCATTATTTTGTCCATGTGTATTGTATCCTTTGGACAGGAACATTTCTGGGTTAAAAACTTTGAGTTCGGGGGGTGGGGGGGGGAACATCCCTTGACAGGGGATCATGCCTATCTATTGGAGATGGTCTCTACATGTTCTATACCCCCTGCATTGTGCATTTCAGCTAATGTCCCCATTCAGTCCTGGGAGCCTCTCACTTCCCTGGCAACTAGGACCCTCCAATGGTTACCTCCAGTTCTGCATTCCCTACTGCTACATGGAAATGAAGAATTCTTAATTAATCGTCAGTATGAAAGTTGTTCCCTTTGTACAGTACCTCATGGGAGCTTTTCCTTCCAACAATGAGGTTCATAAGACCACTTTTTAGGAAAATTAAAATTATTTATATACCTTAGAACTATTATTTCTGGTGTTGATTTCTCCCCTCCCCTTTTAAATGACTCATTTTTATTAGAAAGTAAGTGGTACACCTTACAGAGACTGTCACATACTTTGGCTTTAAGAGTTGTCCTGGTAGGGATTGGGGATTTAGCTCAGTGGTAAAGCGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTAAGAGTTGTCCTGGTAACTAAGGGATATGAAGCTCAAGACCCACAAGTCCTAAGTTTCTCGTCAGGATTCTGGAGTGCCCATCAGGAAACGTGAAAAGCTAACCCCCTATTATACGCCTTTATTTTATCTTCTCTCTTTACTCCCCAGAAGAATACCTAACAATGCTCTTCCCTCTCTCCACAAGCAG
Seq C2 exon
GACTTGCTTCCGCTAAGCCATATCTCGTGACGTTTCTGGAGCAAACACAAGAGCCTTCAGATGTGAAAGGAGGAACGGCTACCATTAAGCATCCAGGTATGTCTAAAGGAAGGAATCAGAGAACAGAGTGGGAAATTCTAAGATCTAATATTAAGTCACTGAGGCATAATATTGTGGTATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056694:ENSRNOT00000081054:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.233
Domain overlap (PFAM):
C1:
PF0135222=KRAB=WD(100=91.1)
A:
NA
C2:
PF0135222=KRAB=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCAGGAAATGTTGTCATTCAGGGA
R:
ACCACAATATTATGCCTCAGTGACT
Band lengths:
310-1748
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]