DreINT0078583 @ danRer10
Intron Retention
Gene
ENSDARG00000011020 | hnrnpa1a
Description
heterogeneous nuclear ribonucleoprotein A1a [Source:ZFIN;Acc:ZDB-GENE-040426-1546]
Coordinates
chr11:2071096-2072898:-
Coord C1 exon
chr11:2072815-2072898
Coord A exon
chr11:2071270-2072814
Coord C2 exon
chr11:2071096-2071269
Length
1545 bp
Sequences
Splice sites
5' ss Seq
ATGGTATAT
5' ss Score
3.91
3' ss Seq
TTTAATTATCTGCTCATCAGGCG
3' ss Score
5.14
Exon sequences
Seq C1 exon
GTGGATATGGAGGAGGTGGTGGAAGAGGAGGCGGTGGAGGATACGGTGGAGGCGATGGATATAACGGCTATGGTGGAGGAAATG
Seq A exon
GTATATCAACAGACAAAAGTAGGATTTATAGTAGTTCACCGTGGTGTGGCAACACACCAGGGTTGTTTCAGCAAAGATATTTTTCAATAAAATGCATTAACTAAAAAAATTAAGTCAAACTGTCACTGATAAACTCACTGAAATAAATATATAATTAGCAGAAAAATATATATATTCGAAGATTTTCTGAATTAAGCACTAATTCAAAGCTAAAAATCTGACCTGCAGCTGTTTATAGAAACCCTTTACTTACAAGTACATCAGGCAAGCACATGATTACTTTATTTATTTATTTATTTATTTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATACATATACATCACTTTTTTTTTTTATATCTATCTTAAGCGAATTGTTTAATTTAAACATAGTTACATTCTTTGGACCAACTAAAGCCATAATTCATTTTTTTGAGTGTGACAGTCTCCAATATGCCACAATAATCATCGAAGCCTGAAAGGGTCAGTTTGAGAGAGTTAGAAAACACTAATTGTGTGCTATTTTAAGCTGAAACTTCACTACACACACTGTAGGCACATCAGAGACTTATTTTACATCTTGCAAAAAGGGGCAAAATATGTTTCCTCTAATGCCGAGTTCAGACTGCGTGATTTTAGTCCTGATTTTGACCGACAGGTTTTGAGAAATCGCCGACAAATGCCTGAAATCACAGGTAAATCGGTGCTCGTGCACGTGAGTGACAATCACACAGTATGAACCATCAGAGACGCGATCTGAGAGAATCGCCGATGAGTCTCCGATGCATGTGAGATATTTGGCGTGCTGAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTATTATTATTATTTTTTTTTATATATATATATAGAAGCTTTAGAAATTAAAAATGTAACCAGGAAATATGTTGTGACCATTGTATTTGTTTACATCCCTTCAAAATGGTCTATGATATGCTGTTAAGCCTGAATTTTGTTCTAACTTTTGCTAGTTCGTCTTGGTTTTCAATACAAACGTATCTTAATCTATGCTTTCATTTGGTCTCTGGTAATTTGCATTTTTAGTAGTGCACTTTTAACTTTCAAGTAAGAATTAATGAGCATTAAAGTTTAGATGTTTGATATTTTGGCTGTACTCCGTATAATTTATGCTTTAAATTTGGGCAAACTATACAAAACACACTACGAATATATTTCTAAAAATCTATGCTTTCAGTCTGTCCCTGATCACATGCATTTTAAAAGAGGGTTAGAGTATTTTCAGCTTCCAAGTAAGCATTAATGAGCATTGAAGTTTAAATGTTTGGCATTTTAGCCATATTTATTGTTAATGCTTGCATTTTGGGCAAACCCTACAAAATTTATCATGTTGATATGATTGCTATGATGTTTGATTAATCTGTTTAATTATCTGCTCATCAG
Seq C2 exon
GCGGCTATGGAGGAGGCGGCCCTAATTATGGTGGTAACCGTGGTTACGGCAGTGGTGGGGGTGGAGGCGGCGGCGGTGGCTATGGAAACCAGGGTGGTGGCTATGGTGGCGGCGGCTATGATAACTACAACAACAATGGTGGTGGTGGAGGAGGAGGAGGCAACTTTGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011020:ENSDART00000018131:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.169
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TGGATATGGAGGAGGTGGTGG
R:
CTCCAAAGTTGCCTCCTCCTC
Band lengths:
254-1799
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]