DreINT0078585 @ danRer10
Intron Retention
Gene
ENSDARG00000011020 | hnrnpa1a
Description
heterogeneous nuclear ribonucleoprotein A1a [Source:ZFIN;Acc:ZDB-GENE-040426-1546]
Coordinates
chr11:2066794-2070954:-
Coord C1 exon
chr11:2070814-2070954
Coord A exon
chr11:2066903-2070813
Coord C2 exon
chr11:2066794-2066902
Length
3911 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
GCTTATGGTCATCTTTATAGGTG
3' ss Score
7.94
Exon sequences
Seq C1 exon
GAAACTTCGGAGGTGGCGGAGACTACAATGACTTTGGAAACTACAATAATCAATCTTCCTCTAACTACGGCCCAATGAAGGGAGGAAACTATGGCGGCGGCGGAGGTGGTGGTGGAAGGAGCGGTGGTGGACCATATGGTG
Seq A exon
GTGAGTGAATACTGTAATTTTGTAGTGGTTTATTCAGAGCAATGCAATCATGCTCTTATACACTACAGGTGTTCGAACTACAGGTGACCCTGTACCACGAAATCACTCAAGTTAATTTTTAATTTGAGATGTGTATATGTACATGTATACATGTTTTTATGGGATAGGATGATATTTAAATAAAACAAAAAAAAAATCAGGAGTCTCTTTTAAAATTTAAATTAAGAAAATGGCTTTGAAGTTTATTTTTTTAGCTATGCCTATAAAAAAAAGAAAAAAAATATATAATTTTTTTTATAAATTTTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTCTTCATTTGTCAAGTAAATCAGACATGTTTTACCTAAAAATTAACCGTTTAATAATATAATTTTTACTCCTGGCTATGCCCATGTACTATGATTTTGGTTCGATGTTTGTTCAAACAATTATTTATATTTATATGTTTGCACAAGAGTTAATGTAAGCTGTTAAACAATTGTTTTGTGAGCTCTGCTAAACAAAAATTACTAAAACTAAATGTATAAGAACTAAATAGAAATTGTTCACAAAATAAAAATTAAAAACAAATCAAATAATGAAAATGACAAACTAAACTGAGATGTACAGCAAATTTAAAAATACGATGGAGTAACTTAAATGCAAAACTATAATACCCTGGCAACATTCTAAAGCCAACATTCAGTTTTATCAAACTGATTTTATTAAGTTAATGCAGTAAATAAAAAATATTTTAAATCAAATTCAAAGTTTAATAAACACTTGCTATATTTGGTACAACGTATGAACTTGCTCTCTTCTAGCCACATGCACAAGAGAGTGCAGAAACCAGACTTGAAAGGGGGGCTTGTCTAAAATTATAGAAATATGTTAGACACTTAAGGCGTCATGTCTGACCATGCAGAGCTGAACAGAAGGAATGAACCTTGGAACCATACCCACATATTATGCAACTTTCAATATTAGATTTTTTTTGCAATGCTTCACCATTACCTCTAATAAATCAATTTGTGAATTAATAATTTTAGGTTAATTTGAATGACTTTGTAGTAGAGTGCGTCCACATAAAACAAACTAAACCCAAGCATGGAGGAATACAGCAGAGTAAATATACAAGTGGAATAAAACCGGATCCATGTACAATGATCAAATTTACAATAAAGCTGTATAGTCTTCACTCTTTAAATAAAGAACAATTAATCTTGAGCTATAAATGTTATTCCAAATGCTTTAAACTTAATGCTCAAACAGTCACAGGCCTTAACAACAATCACGATTTAATAAACTTTCACTTTGATGGTTAAACTCAAATAGACTAAAGTCCTGACCAATAATCCTGCTAAATCAATGTATTGTGCAGTGGTATGACGTTTTGTTTTTCAGTATGAGACTTTTTCCCATCTCCAAAAAATGTACAAAAGGGTTTCTATATGATAAATAAGCTTGAATATTAAAGAAAATGACTTGAACTTATTTAATTACTTTGCATCTTAATTTAACCCTATAACCACAGTAAACAAATTATGACTTTATCTGTTACTGACTCTTACTGCCAGTCTGCCACACCCACTTATTTGCATCTTGCAATATACAACATAAAAAAAATACATAGATTTTATGGTACACCTTTCATTTTGCTGTAGACTATTTAAATGTGGTCATGACCTATGAACATTTCATCTCATCAAACTATTTCATATCTGCCATGAGGCTATTCAATCGTAACAATGTTAAAACAGCTGCCATAACATTATCAGTGTGTGTGTGTGTATGTGTGTATGTATATATATATATATATATATATATATATATATATATATATATATATATATATATATAAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATACATACACACATACACACACACACACTGATAATGTTATGGCAGCTGTTTTAACATTGTTACGATTGAATAGCCTCATGGCAGATATGAAATAGTTTGATGAGATGAAATGTTCATAGGTCATGACCACATTTAAATAGTCTACAGCAAAATGAAAGGTGTACCATAAAATCTATGTATTTTTTTTATGTTGTATATTGCAAGATGCAAATAAGTGGGTGTGGCAGACTGGCAGTAAGAGTCAGTAACAGATAAAGTCATAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGGCGTGGTGTATGACAAAGTTTCAGTCGCATCACTCTCACTCAAGGAAATGTCTACAGTAAAGCTGCACAGGTCGTTCACATATCATTATAAAAGCACGTCTCACAATACAGACACGTTACACACATATACATTGTGATATATATATATATATATATATATATATATATATATATATATATATATAAGCCTCCCACTTATCCTCTTAAAAAAATGATGTAATTTCTGTTTAAATAATGTATTAATATCGTCTTAAATTTTGCATAAACGCATCTTGAGTCTAAACTTGTGCATGATGAATTGCGTATTAAGATGCAGTTATAAGATATCAGTCTTTCGGATGAGACGCTAAACCGAGGTTCCGACTCTCTGTGGTTGTTAAAAATCCCAGGATGTCTTTTGAACCCCTGGTTTAATCCCGGCATCCTGTCCAAATTTGCCCTCTGGCCTTCTTCCATCATGGCCTCCTAACCCTCCCCATATCATAATTGGCTTCATCACTCTGTCCCCTCTCCACCAATCACTGGAGCGTGGTGTGCGGTCTGGTGCAATGTGACTGCCGTCACATTATCCGGGTAGATGCTGCACTAGTGGTGGATGAGGTAAAGCGTTTTGAGTGTCCAGAAAAGCTCTATATTAAATGTAAGCGATTAAAAGATTATACAAGCGAATAATATCAGGTGTATACGGGATATTGATTTTGTGCAATATTTTTAAAATAAAGTTTAGTTTTGTAGTGCAAACCGGGACCATTATCGTCAGCATTTGCTGTCTTGTGATTAAACGCAGGGTGCTAATGTGAGCACGCACTGACGTGCCCAAACACGGTCCTGGAGGGCTGGTGGCCTGCAAAGTTTAGTTCCAGCCCCAATCAGACACACCTGGGCAAACTAATCAAGCTCTTACTAGGCTTTCTAGAAACATCCTTGGAGGGTTAAGGCAAGTTGGAGCTAAAATATGCAGGACACCCTGGAGTTTGGACACTCCTGATCTATCCCATGACTATTTTCTCCCAAAAAATGTAGTGTTTTTTTTTTTTTGAACAGTGGTCTACAAATGTTCAATGCTTATGGTCATCTTTATAG
Seq C2 exon
GTGGCTATGGAGGAGGCTCTGGAGGAGGCGGTGGTTATGGAGGAGGATCTGGTGGTGGTGGTGGAGGATATGGCGGAGGCTCTGGCGGACGGAGGTTTTAGATTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011020:ENSDART00000018131:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.542 A=NA C2=0.364
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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]