DreINT0106142 @ danRer10
Intron Retention
Gene
ENSDARG00000000796 | nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:ZFIN;Acc:ZDB-GENE-040704-11]
Coordinates
chr23:32228916-32231334:-
Coord C1 exon
chr23:32231237-32231334
Coord A exon
chr23:32229710-32231236
Coord C2 exon
chr23:32228916-32229709
Length
1527 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
GTTGTGGTTCTGTTCTACAGAAA
3' ss Score
7.5
Exon sequences
Seq C1 exon
GAGAAAAGCGTCTTGTCGTGGCAGGGGACGTTATACATGGTTATCCAAATCTTGGAATACGGACACTTATAGGTCCCCCATCACATTACGTTTCTCAG
Seq A exon
GTAAGCTGCTTTTAAAATTCGCCAGACAGTTAATAAGCTAATACTGTTCTCTTTATGTTTGTTTGTGCTTCTTTTTAACACTGTACGAACAGCAAATGTAGTTTGTAGTTATCCAAAATAGAGTACGTATTTAGGAATCAAAGTGTTTATGCTAGCGAGGTGTAATTTTATTATTATAGTATTGTGTACTCTTATGAAGCGCGCGAGTTATTAGGAGAATAGCGCTTTATTTGTGTTATTCAAGACAATAGATGCGTAAAAACTAGTTGGCTATTTAAAATGTAAACTAGTCTTTAAAAGTGTGTGTATAAGCAGTGTTAAACAGTATGAAATGACAGAGGGGGTGTGTGTTACAGTGCGCAGTGCACGCGCTGAGTGTAGCTGCAACAGGTGCTCGAGCAACACCGGACAACTTATCTGCATACTGCTTTAAAGTACTGACTGTACTCAGGATATTTGGACAGTCTGTTAAACGATTCATGTATATTAGTAGCAATTCATTCGATAAGAAAGGAAGAAAAACATTTAATCATGTAAAGTTTTTTTTTAAATGTAATCATTGTACAAACTAGAGAACTGGGTACTTCGTTGTGTATTTATGGAAATAATTATATAATTATGAGGTTGACTTATTTGTGAGACAGTATCTGTTTACATTTTCATTCAATTAATTATAATAATAATAATAATAATAATAATAAGTAAACAGAACTTCTTTACTGCCTATTTTATTTATATGTAATAACAATATGCTAAACTAATATCTGGCCAACGATTTCGTACATATAAAATAGTGTAATTTTGCAAACTGTTATATATTTTACACCACTTAGACACACCACAATAAAATTTATATAGCAAATACATTTGCTGTCAAAATATTTGTCAACATGTAGGCAATGAAATGTTCAGGGGTCAAATGGTCATCGAGTGTCATGTTCTCACCTTGCCCTGGGTACAAGGTTATGAATGTCTGTCAGGCTGCTGAGCCATAATTGTGTTTCACATTGCATCGTGTTAAAGAACTTTCTGTGGAGTGATGAGTTTAAATCTGATGTACAATTTTCTAAATATTTTCATTGCCAGTGCATTTTCTCATTGCAATAGTTTACAGATTTAGATGGGTAATAATAGAAATGCAGAACGTTACTGATTATGTTTACTATCACTTACCTAATGGCACACCTGGTTTTAGTTTGCTGGGGAAATTTGTGTCTATCTTAAAAAGTTCCATATACATAAACCGCCCACTCCCATGTCCCCTTACAAACATAACACGCCCTCTCGGTGAGGCAACATGTGTCGTGTCTGATGTTCTTAATGTGGTAACACAATAAGCATGGCTGCCCTTTCCAGCCAGACGCCCCTCCAAGTTTTCTCAGGAATCTTAAAGCACTTCAGAGAACTGTGTGTATACAGACTTTCTGGCCATCGAGTAATATAGTTTAGGAAGCTCTCTTAAGCTCTCGAGGCATTAGATGTTCCTACGGTATTGAAAAGTAGATATGTTGTGGTTCTGTTCTACAG
Seq C2 exon
AAATGACCTGTGTTCAAAGTCAACATGGAGTCCAGTCCTACGAGAGCTCCCTCTTCAGCTCAGAGTTTCTGAATCCTGACTTCACCTCCAGGTTGGCCATGGATGTGACCGAGCAGCGGGAACAGCTCTCTGCGCCCTCCCTACCCAGCATCACTTCTCTGGTTGGGGGATACGTTGGCGAGTTTGACACCTACTCATGCCAGATCGCCACAGGAGCTGCTTCTACCTGTGTGGGCAGCACCTCCGGGCAGCTGGACTCCTTCAAGCTGGATGACCTCCAGGTGTATGGCTGCTACCCGGGCACGTTTGCTTTGAGCTACCTGGACGAGACGCTGTCCTCTTCGGGTGGGTCAAACTGCTTTGGAAGTCCGGCATCTGCACCGTCTCCCTCCACCCCGGGATACCAGCACATGTCTGCATGGGACAGCACCTTTGGTCCCTGCTCTCCTGACGAGGGTTGCTGGGGTTCTGAGAAGCCTCTGAACCAGGCAGCATCTTTCTTCACATTTGGGCACGTCACGGCTGATGAGCTTTCCCCACTGGGACAGATGCAGTCACAGATCCCAGATCAGGATCCCTTTTCTCATACTCCGCAACATGGTTCTCCACTTCCCTTCAGTCCACTCAGCTTAGAGCAGGGCAGCCGGGATGGATCGGGACTGATGGACGGACACTTGTCTCCTAAAGTGAGGAGCCCCACAGGAAATGAGGGACGCTGCGCCGTGTGCGGAGACAATGCTTCTTGTCAGCATTACGGGGTGCGCACTTGTGAAGGATGCAAAGGCTTTTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000796:ENSDART00000000876:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.282
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0010513=zf-C4=PU(38.6=10.2)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTCCCCCATCACATTACGT
R:
CTCGTCCAGGTAGCTCAAAGC
Band lengths:
357-1884
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]