DreINT0129987 @ danRer10
Intron Retention
Gene
ENSDARG00000005593 | rxrga
Description
retinoid x receptor, gamma a [Source:ZFIN;Acc:ZDB-GENE-980526-36]
Coordinates
chr2:21107694-21109861:+
Coord C1 exon
chr2:21107694-21107873
Coord A exon
chr2:21107874-21109700
Coord C2 exon
chr2:21109701-21109861
Length
1827 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
ATTGTGTTGTGTGTGTGCAGCGG
3' ss Score
8.18
Exon sequences
Seq C1 exon
GGAAACATTATGGTGTTTACAGCTGTGAAGGATGCAAAGGCTTCTTCAAGAGAACCATCCGTAAAGACCTGACGTACACTTGTCGAGACAATAAGGACTGCCAGATAGACAAACGCCAGCGAAACCGCTGCCAGTACTGTCGCTATCAGAAGTGTCTCGCCATGGGCATGAAGAGAGAGG
Seq A exon
GTGAGTGTTCAGTTGATATATTCAATATTTTGATAACAACACAAGACAGTCGTCTGATTAGGAATCAATCATGCAGACAGAGATTTTTGATTACTTTTATCTGGCTAAAGTTACTCATAGTGAATGCAAATCAAATTAAGACTTGCATTATTATAGTGCAGCAGTACCATATATACATGTAAGTACCACACTTTTAATGTCTTTAAGATTATTTGCTGCATTTTTTGAAAGGATTCACACATGGTAATGGTTTATATCCACTGTTGTCTGTTTGCACATACAGTACTAAAGCAAAAGTTTTAGTCTATTTTTAATTTGCTGTTTTAGTGATGGTACTGTACATTATTAATGCCACTGTAAGTTTTTTTTTCATTTTCAAATATTTCCCAAGTGATGTGTCAAGTGATATTTTTCTTTTGGAGAAAGTCATATCTTTTAGCTCTTTTTTTGACTGTAGAAACTGCTAAGATCAGTAATATTAGCCTCATAATTATTTTTTTTATTGGCTAAACAACAAACCTCTGTTGATATGATATATCAATTAATCAAATATGCCTAATTAATCAAATTTACCGAGTTAACCTGATCAACAACCTAGTTAAATCTTATATCTTGCAACCTCACATGAGCAGATACATAAAGTATCTTGCAAAATAACTAGTAAAACACTATGCACTGTCTTCATGGCAAAATAAATGAGTTATTAGAATTTGGTTATTTAAACTTTTATGTTTAAAATGTGTTGGCAAAACACATCTCTCTGTTAAATAGCTCTTGGGAAATATTTAAAAATATTTAAAAAAGAATGATCAAAAATTTAGTTTTTAACAGTATCATTTTTTTTATTCAATTATTACTATAAATGCAGGTTGTATGTTGGTTTAATTAATAGGGTTATGATTTGTTTGTGTAAGACATGAGAAATACAGAGTTAGAGAAAGGTTAAGAATGAGCGCTTGCTGTCTGTAGTGAAACATGGTGGAGACTTGGTCTTGAGATTGGTTTGTGACTGTATTTCTTCCAGTACTGTTGACAAAGCTTGTCTGAATTGACTGGATTGCGAAGGCTGAAGTATACAGACATGTTTTAATCCATTATGCCATTCCTTCTAGACAGCACCTTGTTGGTAATGGCTTTATTTTTTAAGCATGAAAACAATCTTAAAAGTACTGCTAATGCAGTGAAATCATAATTGGAGTAAAGAAAAAGTTGATGAAATACAGACAGTCGTAAAATGGCCTCCACAGCGTCCAGACTTAAATATTACAGAGACAGTATGTGGTCACCTATGCAGAAAAAGGAAAGACAAAACAGCCTAAATCTTAGAAGTGAAGAAAGATTCATGGTATTACAAATCACATTATTTCAGAACATTTCAGGACGGCCGCCTTAAAAAGAAAATGTGCTTGTAGCCAAAGGGAGGTCACAACATAGCTTGAAACAGTGATTTTACCTGAAAATTGTGTTATTTTTTGGACATATTTCCCTTCATTTTTGTTTGTATCTTAAGAGATTGTGAATTGCAAACCGTATATTGATATGTGAAATCCTAGATGAAATGTCAAAGGCATTGAATGCATGTATTTATTCATTCATTTTCCTTTGGCTTAGTCCCTTATTTATCAGGGGTTACCACAGCAGAATAAACCAACCACCATTTCACCATCTGTTTTACGCAGAGGATGCCCTTTCCATCGCAACCCTGTACTGAAAAACACCCACACACTCACATTCAGCAACTTCCTTATCATAAAATTGCTCTGTTCAGAAAAAGGTAAATAATAAGGTTTGTGTGTTATTATAGTTGATTGTGTTGTGTGTGTGCAG
Seq C2 exon
CGGTCCAGGAGGAGAGGCAGCGCGGTCGGGAGAGGAGTGATAATGAAGTGGACTCCAGCAGCAGCTTCAATGAAGAGATGCCGGTGGAGAAGATCCTGGACGCTGAGCTGGCAGTGGAGCCCAAGACAGAAGCTTACATGGAGTCAAGCATGAGCAACTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005593:ENSDART00000021168:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
NonCoding
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTATGGTGTTTACAGCTGTGAAGGA
R:
CGAGTTGCTCATGCTTGACTC
Band lengths:
334-2161
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]