DreINT0078576 @ danRer10
Intron Retention
Gene
ENSDARG00000011020 | hnrnpa1a
Description
heterogeneous nuclear ribonucleoprotein A1a [Source:ZFIN;Acc:ZDB-GENE-040426-1546]
Coordinates
chr11:2064964-2066902:-
Coord C1 exon
chr11:2066794-2066902
Coord A exon
chr11:2065031-2066793
Coord C2 exon
chr11:2064964-2065030
Length
1763 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GCAGTTTGTTCTTTTTTCAGGGA
3' ss Score
8.87
Exon sequences
Seq C1 exon
GTGGCTATGGAGGAGGCTCTGGAGGAGGCGGTGGTTATGGAGGAGGATCTGGTGGTGGTGGTGGAGGATATGGCGGAGGCTCTGGCGGACGGAGGTTTTAGATTCCAAG
Seq A exon
GTAAGAAGTGGTCCTCTTGATGAAGAGACCTCTGAAGTTTGTTTTTAGCTCATCCATGTCCAAACATCAGATAAGATGCGTTTCCAAAGCAAATGCTAGCCCGTAATGAATCTTCAATTGGTGGATAAATGAGTAAAAGCCATTGAGTTTTCAGTGCAGGGGAGATCCAGCAGCAAACCTTCAAATCTTGTTAAGCTAAGATCCAGACGAAATGTAGATTTTCTCTTTTCGCTCTCCAAAGCTTGTGGCTGCAGCACATGCAGACTGATCCCCTCTCTCAATGTCCAAACCATGCAGTCTTAGCTGACCTGAAGGTTTGCTTCTGTGCTTCTACTACTCATTCCCCTCCAGTTCAGCTCTTGATGAAGACAAAGCGAGGATTGCAAAGTGTAACTGAATTTATGTTCCGTATTGTCCAACAGGCCACAGTACTTAGAGGAGAGCCAGAGAGAGATGACAGGGAAAGGAGAGAAGCAAGCAGGTTTACACCTAGATCTGCCCAGCCAAGCAGTGTGGTGGCGATATTAACGTCTGCCACATGAAGAGAACGTGTTCAATAGGGGAAGAAAAAAATCATGTGGGAAGGACGGGTGGGAGTGGGATTTGGGGGGGGAGAAAAAAAAAAAAGGAAAGTTTCAAAAGTACTCTTGTCCTGGAAAGACATTTACTAGTTTGTAGTTTCCCTTTTTTTTTTGTCTGTGAAGTGCAAAGCATTCCAATGAGGTTTTATGCAGGGTTTAACTGTTGTGTTGGCTTTTCTCTTGAACCAGTAGGGTGTCTGTCCTTTTCTTTCTTTGCTTTTTTCTTTTAAATGTAAACAGTCACCAATCAAGATGAAATAAACCGCTCCTGTTTTTTTATTTAATTGCATTGCTCAGTGTTTTGATTTGATTTTTACGTCACCCAGTTGCACAAATGACCAAATTTGACGTCTCAGCAACAAAATCTGCTGGATGTTTAGATGACGTAGACTTGAAGCGATGCATTAATACGATTCGGTCGCTGCAAATTTAGATCCTTACTGGTTTGTTTGAACATCCATGTGAAATTACCAGTAAAGAAATCCGAGTTTAACTTGAACAAAAGCTTGGATGGCTTATTTTATCCTGTAATTAGCACACGTTCTGGTGTTTTTGCAACATGTGGGTAGCAAAGTAGACCAATGATGATGCTTTGTTTGAGTGAATGAATATCCATAAGAGGATTTTAGCAGCTCTCTCACGTAAGCGAGCGGTCAGACTATCCCATCAAGTGCCAGCAAAGATTCTAGGCGTCTGGAGGAGCCAGCTTAAAGAGCCTAGCCAAAGAGAAGAGACTGTCCATCGAAGAGAGGCTAGCCATTGGGATGAGCCAGCTGAGAGGCTAGCTTATTGGAGCCGCCAGCAGTCTTATTGAGAACAGATGTGAGACTAGCGAGAAACAGCTACCAAAGTAAGGCATATTACATACCAGACTGGTAGGTAAGAGGCGCATTTTAGTTTCTCTTTCATGTGAAATATTTGTGCTCATCACAATTAGGAGTAAAGATTTTGTTGCTTGGTTGTTTTTTCGTGGTTGTGGTGATGAAAACATGACTGCCGAACTATTACAGTGAGCTAATCTTATAGTAACTGTGTTTTAAAGTAAGGTTCGGTTATCTAAATTTGATGTAGTCTTCTGTGTCAGTGGTGCATGAGACACTTGTTACTTCAGACGTTCTGTGCTTGGTCTTTCGCGTGTCTCTCCTAATGTTGATTTTTAAAGGCAGTTTGTTCTTTTTTCAG
Seq C2 exon
GGATATAATGGCTGGATTTTATGCCTGTGGGACCGAGCAAACTTACCAAGGGCTGGTGGTCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011020:ENSDART00000018131:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.364 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]