DreINT0106147 @ danRer10
Intron Retention
Gene
ENSDARG00000000796 | nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:ZFIN;Acc:ZDB-GENE-040704-11]
Coordinates
chr23:32224802-32227258:-
Coord C1 exon
chr23:32227080-32227258
Coord A exon
chr23:32226179-32227079
Coord C2 exon
chr23:32224802-32226178
Length
901 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
ATTTTAACTGTGACCAACAGATC
3' ss Score
6.04
Exon sequences
Seq C1 exon
GTCAAACCCTGAGACAGACAAACTTATTTTCTGCAATGGTGTGGTTTTGCACCGGACGCAGTGCGTACGAAGCTTTGGTGATTGGATTGACTCAATTATGGAGTTCTCTCAGAGTTTACATCGCTTGAATTTGGACATATCTGCTTTTTCCTGTCTTGCCACACTGGTCATAATCACAG
Seq A exon
GTAAATTACTGCAATACCAACTGCTTCATCACAGACTGTAAACAATATCTGACCCTGGACCACAAACTCAGTCTAATGGTGCACAGGTATATATTTGGCAATAGCAAGATGCATTGTAAGAACAATATTGATTTTCCCTTTATGCCAAAATCATGAAAATATTAAGTAAAGGTCATTTTCCATAAAGATATTTTGTAATTTGTTTACCATAAATATATAAAAACCTCAACGTTTGATTAGTAATCAGACCCCCTAGTTTTTCACGATTTATTTTGTGATATTTTGAGATAAAAATGACTTTGCAGATAATTTTTCAGGGGAAAAAATGCACATAAATAAATTTTATTTACCGAATTAGGAAGCCTACTATGTTAGGTGTGAAATCTGACACAATGACACTAATAAAAATAAAGCTTCTTGATTTTAGTGTATTGTCAAGACAAAATATAAAATTGTAGGGATTAAGTCAAAGAAAGGTTGTTTACAATAAATTGCAAACTGAAATAAATATAATTTGATTATTTGGTTTGGAATTGGATGTTTTTTTTTAATGAGATTAACGTTTTTTGCGTTTAATTATAAATTTCCCAGGATCGCAAAAATGTGTGACTTTTTGTAGTTTTTGCGTTGGATTCAACAATTGCGGAATCACGAAAACTAGGGGATCTATTCGCAATGAATATGCAAAGCACTTAAATTGGACAACTTTAATCAAATTTTTAAAAAAAATTGAGCTTGCAGATTCCAGCTATTCAAATAGTTCTATCTTAACCAAATATTGTCTCATCTTAATAAATGAAAGTTTCACTTTCCAAGAATGCACATGGTTTTATGGTCCAGGGTCCCACATTATGTTTCATCCCAAACAAATATCATCCCTAATTTTAACTGTGACCAACAG
Seq C2 exon
ATCGACATGGCCTGAAAGAGCCCAAACGGATCGAAGACTTCCAAAACCGTTTGATCACATGTCTCAGAGACCACGTCTCCACAAGTGCCCTTGAGGTCGGCCGGCCCAACTCTCTGTCCCGACTGCTGAGCAAGCTCCCAGAGCTGAGAACACTGTGCACCCAAGGCCTCCAGCGAATCTTCTATCTCAAACTGGAAGACTTGGTCCCACCTCCACCCATTGTGGATAAAATCTTCATGGACACGTTGCCATTCTGAATGTGACTTTATAAATGGACAACCAGGGTGATGAACTGAGGATATGGGATGTTTGGGGAGCTCTTAAGGGTCTGACTAGTCAAAGGACTTTATCGCTTACGGTTTCTCTGCTTTCTTGGAAAGGGAGTCAGAGAAGGATGACATTCTACTTAACGCCTGTGTTTGAAGACCTTCATCGCATCGTCTTCAACACTGAACCTACTAAGTGACTGTATGCATTCAATAGACATGTCATTATCAGACATGGACTTTCAAATCTTAGTGTGTTTCAAGCTGAAATGGTGGCTTTAGTCGGTAACATTTCAGGTCAATGGTGCAAATCAAATGCTCTACATGTGTGACTTCTGAAAGAAATGATATTCCCATCAGTATTACACCAATGTTCAGAGAGCATATTCCAGATGAACAGCATCCAAAGATCCATCTTCAAGAAAGAAAGGCCATGGACCAAAACAAGGAGTAGAAACAGCATTTATTTGGATGCTTAAATGATCAGACAAAGCCTTAAATACATTCAAGTGCCGAAGCATTATCTATCTTAAAGGGGCTATATGTAGAATCCAGAATCTAAGGCCACTGGCTTTTTAATTAACCAGTCATCGTCTTATTCACAACACAAAATAGACAACCTAGGTCTCATTTTCAAGTTTTATTACAAGATTAATACATCCAGTCCCTTTAAAAACGCTCAAAAATGTGCTCAAACAGAAAAACACTCAAACACTTGAGAACAGGATTGATGTGAATGCATTCGGGTTGACTTTGCTAATGTTTCTAGAAACATAAGCGTGTATTTTAACAGTGATTAGTTCATATAAAAGGTGGTGTGAGATCCAGTGCAGCTACTGTACATGTACAGCCTCGTACACATGCAAATACTTGGAGTATTACAGATGCCTGGCTTAGTGTGCGGTACCAGTCAGACTATAGAAGAATCATATTTGTATGTATGTATTTTGAGGATGTAAATGTTTGTTTAGAGCTTCTGCAGACTATTTTTTTTCCGCATATTGAAAATCAAGATCGGGCATTCTCAGTTTTTTATATATATAAAATGAGAGGTATTGCTTATCTTTCATTCATTTTGTGCAGCTCTATATGGAATAAATTTGAAACTAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000796:ENSDART00000000876:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(30.3=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(34.3=79.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTCCTGTCTTGCCACACTGG
R:
AGAGCTCCCCAAACATCCCAT
Band lengths:
354-1255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]