BtaINT0072905 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021580 | HNRNPA3
Description
heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:HGNC:24941]
Coordinates
chr2:19703803-19705981:-
Coord C1 exon
chr2:19705913-19705981
Coord A exon
chr2:19703929-19705912
Coord C2 exon
chr2:19703803-19703928
Length
1984 bp
Sequences
Splice sites
5' ss Seq
GCAGGAGGT
5' ss Score
-3.11
3' ss Seq
AATGTATTGGTTTCTTTCCTCAG
3' ss Score
-9.91
Exon sequences
Seq C1 exon
ATGGAGGTAAAACCGCCGCCCGGTCGCCCCCAGCCCGACTCCGGCCGTCGCCGCCGCCGCCGGGGTGCA
Seq A exon
GGAGGTATTAGGGGGAGAGCGGGGGGTTGCTGGGTAGTGGCCGGCAAGATGGGGGGCCTGGCTCGGTGGGAGCGGGGAGGCCGGGTGGACCGGGTCGGCCGTCCCGCGCTCTGCGTGGAGACGGGCGCTGGGAGGGGGAGGGGAGCGGGCCTCGGAGCCCTCCTCGGGGCTTCTCGACAGCCTTGCCGGCTCCCTGGGCTGCACGAATGGTCCCTTGGAGATGCGGTGTGGCTGGGGAGACTTCGGGAGCGGAGCTGGCCCGCTGGCCGCGCGGCCTCGGATCCGAGGCCGAGGGCGGCATGGCGGGCCTCGGCGAGAGCGGTTGGGAGGAGGCGGTGGGGGAGGGGAGGGGACGAGCAGGCACATCCGGGCGAGCGAGCAGGCGGGCGGCGGCCACACTGACATTGATCCGCCGCCGCGTTACGAAATGGCGCATTGGCACGCAATGGCCGCCGCCTGGCTCCGCCGCGGGAGAGAGCGTGGGATTGGAAGGAAGAGGGAGGAGGCGGCCCAGCAGAGAATGCCGCAAATGGCCTCGAAGCTTGCGGCCTGGTGCTCTCGGTGATGTTCTCCCGACGCGTTTCTGGGCCTTAGAGATCTCTCAATGGAGAATTTTATGTCTTGTTCTGTACCTTGCAGCACTCGGTTCAAAACATGAAAATTTTTTTTTCCTGAAGTTTACTGTTTTAAAGTATTTTTTGAGCTGCCATTTTTGCTAAAGTACTTAACAGTGTTAACACGTAACTAAGCGCCATGTGGGTGAAGTATTCTATCTCGAAATTTGAGTGTGGTTGTAACATATGAATTTGAAAATTTTCTCATCTTTTTTTTATTCTCTGATGGGTAGGCTCTGGTTGTAGTTCCTTGGAAATTTATTTTCCAGGCCTGCAACCAGAGTCGAATTTTTCATTTGTTTGAGAAAATTCCATGTGGGTTGTAGTTGTTTTCTTATGTCAACTTTGCGTTGTCGTCGATTAGATTCATTTAACTGGGCCTTGGAAAGATGAAATTAAGTGAATTAATGCTTTAGGCTATTAATCGTTTAACATTTTTTCCTAGCATGTGACAACCTCTTCATATTAAATGCCTTAGCGTCTCTACTTTTAGAAGACACAGGAAGACCTTAGAATGTAATGTATTTAAGCACTTTTGATGAACGATATCTTAACGCATATGTGTATTAAGTGGCTGTTCGTGTAATTTATTAAAGACGTAGTTGAAGTATAAAACAATTCAGGCCATATGTTGATTTTCTGTAAATCTCAAATTTTTGTTTTGTTGGGCTCCTTGTCAAACTATATCGAATACTGTACTTAACGTAAGTCCAAAACTGGTGTTGTGTGACCTAGTAAAGTGTTGGTTTTGATATTTTGGGTATGTGGTAGGAGTGCAAATAGGAAATTTTTATGTGGTAGACTTTTTTCCCCCCACAGGTTTTTTGGTGAGGGGGAATGCTGGTTTTCTCTTTCATTGAGAAATATTTATTTCAACATCTTTATTTGCTTGAAAGTGGTAAATTTCCCTTTAAGTTTGTCACTGGTAACATAAGTTGTGTTTCACGATTTTGTGGTTTAAAATTAAATGCTTTGGGAGGTGTAGAGTCAGGAGGGAAGTTAGGAAGAGAAATGGTATAGATAAAATACTGAATTCACAACACTAATTTCTTAGAAAGTGGTTTCTCAGTAGCCACTTCAAAAATAATCTACCCTCAGGAATTTGTTGTTTTAGCTCAAAATTATGGGACTTCTGAATCTGGAATTCTCTTGGGCTTCAGTTTAGTTTAGAAGTGATGTTGGCATTTCAGAGTTTGGTTATAGGTTTTGGTGTTTGGATTCCTTTAATCAGTTGATATGTATGATTCTACTCTAGTGTTTTAACTGGACAAAGTGATAATGGTACAGGAATTTGTTGTTATTTGTAGGGGATTAAAAGTCTTGTGGATTTTTCACTACTAAACAAAATAAAATGTATTGGTTTCTTTCCT
Seq C2 exon
CAGGGTCATGATCCCAAGGAACCAGAGCAGTTGAGAAAGCTGTTTATTGGTGGTCTGAGCTTTGAAACTACAGATGATAGCTTAAGAGAACATTTTGAGAAATGGGGCACACTTACAGATTGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021580:ENSBTAT00000028757:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.262
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF142591=RRM_6=PU(40.0=66.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGTAAAACCGCCGCCC
R:
ACACAATCTGTAAGTGTGCCCC
Band lengths:
191-2175
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]