DreINT0106187 @ danRer10
Intron Retention
Gene
ENSDARG00000101508 | nr6a1a
Description
nuclear receptor subfamily 6, group A, member 1a [Source:ZFIN;Acc:ZDB-GENE-991207-19]
Coordinates
chr8:52904564-52905415:-
Coord C1 exon
chr8:52905294-52905415
Coord A exon
chr8:52904717-52905293
Coord C2 exon
chr8:52904564-52904716
Length
577 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
ATTTCTGTATATTTGTCCAGATA
3' ss Score
6.14
Exon sequences
Seq C1 exon
TTTCAGTGAGGATGGGATGGAGGTGATGGAGAAGCTGATCTATCTCTTCCGCAAGTTTCACCAGCTGAAGGTCAGCAATGAGGAGTACGCCTGCATGAAGGCCATCAACTTCCTTAACCAAG
Seq A exon
GTAAAACACACACACATCTGCATCTACTGTACATCCCTATACAGCTAAAGCACCATTATGAGTCAAAATTAGGTGCGTTTTCTCCTTAAAACAAGCTAAATAATCTGACAATGTGGTTAGCAAAGTAATCTTACTCCAAACCAAAAACAAGTTTATTTTTTTAACCCGGTTGGCAGATTATTTTGCCTGTTTTAAGGAAAAACTCACTTCAATATGGCACAATATTTACTGTGTGTCTAGAATATGCTTCTTGATTCAAAGATAGATATTTGGACTAAAAAGAAGATAGAAATTAAGTCAGAAAAGCATTTTTTGCAGTGTAACTCGGTTGTCCCGATACTGGAATTTGCTACCAATCTGTACTGAAGTTTTAATAATGTCCATTTTATGCTAACGTTTGAGCACTGCCGAGCTCGTTCTTAAACAGCGCTGATTTGCCATTGTGTTCACGTGCTCAACAGAAATGACTGTGATTGGCTGTGAAGGTCATCAGTTCACTAAACTCTGTAGGTCTGTGATGTCAGTAGAAAAGCAGCTGGTCATGCATCTGACTGGATATTTCTGTATATTTGTCCAG
Seq C2 exon
ATATCCGTGGCCTGACCAATGTGACGCAGCTGGAGCAGTTGAACAAGCGTTATTGGTACGTTTGTCAGGATTACACGGAGTACAAGTACCCTCACCAGCCCAAACGCTTCCCCGAGATCATGATGTGTCTGCCAGAGATACGCTGCATTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101508:ENSDART00000161943:6
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=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(20.3=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(25.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGAGGATGGGATGGAGGTG
R:
TGCAATGCAGCGTATCTCTGG
Band lengths:
270-847
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]