GgaINT1019978 @ galGal4
Intron Retention
Gene
ENSGALG00000001073 | NR6A1
Description
nuclear receptor subfamily 6, group A, member 1 [Source:HGNC Symbol;Acc:HGNC:7985]
Coordinates
chr17:9468309-9469968:-
Coord C1 exon
chr17:9469858-9469968
Coord A exon
chr17:9468562-9469857
Coord C2 exon
chr17:9468309-9468561
Length
1296 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGG
5' ss Score
2.87
3' ss Seq
AGTTGTTTTGTTGACCGCAGAGC
3' ss Score
8.04
Exon sequences
Seq C1 exon
GCCCGAGGCTGGCTGCTGGAGCCGGGTCACAGCACACGTCCCCGGGAGCGCCGCGCAGCCATTGCCGCCTCCTGGCGCCTGTGGACGCTGCGGGCAGCTGTGCACGGCAGT
Seq A exon
GTGAGGTTGTGTTCAGGCTAAGAAAGACCAGAACAAAACCGCCTTACCCAGAGGAAGCGCGGCACAGTGAGATGCAGAGGTGCGGTTCCTGAGTCCTGAGAGCAAAACCCACACAAAGTCCTTCCCGCACCTCACGCAGGGTGTCCGTGTGTGCACATAAGGGCTGACATTTGGGCAAGGAGCTGAGTGAGGGATGTGACGGATCTGTGTGTCCCACTGCACACAGGAGCAGTGCCCACCTTCTGAGCGTGGCTCTGCTTGCACGGCCAGGACTTTGTTAGGTTAAAGTCCTGGGGCAGGAGAAGCGTGAGAGGTTCCTCTGGCCTGTGGTTGCACAGCTGCTGCTGCAGAAGGCTGCTGGTGCAATTTGCTGCCATCATTTTAATGCGGTTAACTTTTAACATGAAGCAGGATTTAGATGTCCCTCAAGATAGTGAGCCTGCATTTGAGTTAACGAAATCGGTTGCTTTAGCCATCATTTACTTTTTCCTTTCCATTTGACATCCCTGTCTATGAAGATTACTGTGTGCTCACGGAGGTTCCTGCTGAGCTGTGCATCATCCCTCCTCTGTCTCAGAGGGAGTGTTACGGTCTGAAGATACTGAATTTCATATGACAGCTCCTGTTGCTGGGGGTCGTACAATTTACATTTTTTTGTCATCCAGAGGCCTTCCAAAGGTTTAGAAAAGGGAATAGTAAAATCAAGTCATGGCAACTTAACCTCATTATCATTTCTGGAATAACACTCAGGCTGTGGGTGCGTGCGTTGTACAGAGAGGTCTTTGTGGGGGTGGCCGTGTCTCCGTGTCCCCCTCCCTGCCCCACACCCCGCTGCCACCTTCCCGTGTGTGGTGCAGCATCCCGCTGATGTCTGCCAGGCATTCTGTGCTTTCAGTGCAGGGACCTGCAGTGCAGTTTGTAACCCAAGAAGCACCCAGTTTTCCAAACTGCTTTACATTTCTGGCAAATCATGACTGAGAAAGAGAGCGTTTACAGAGGCTGTCTTTGAGACACATTTGGGCTCTGTTGTTCTTCATTCTTGTTGTTGCTTACTGAGAATTCCTGGATTTAAATCCTGTGGGATGTGGTGAGCTGAGATGGTTGAGCTGTGGAGCCCTGCGTGCTCCTGGCCCAGCAGTAGGGCTGGCTGGTGCCTGGGCTGCTGGGAGAGGAGCTCCAGCATGAGCACTGTGAAACGTGCTGTTTTGGGAAGGTTTTGGTCTGTGGCCACAGGGGCAGCTCCAGTCCCACTGGGAAAGATGAAGCGGCTCGGTGAAGTTGTTTTGTTGACCGCAG
Seq C2 exon
AGCCCTTTCTCTTCTCTTGCAGATGACCGGGTTGATCAGCGAACCTGCCTGATCTGCGGGGACAGAGCTACGGGTCTGCACTATGGCATCATCTCCTGCGAGGGCTGCAAGGGGTTTTTCAAAAGGAGCATTTGCAACAAGCGGGTTTACAGATGCAGCCGAGACAAGAACTGTGTCATGTCACGCAAGCAGCGCAACAGATGCCAGTACTGCCGGCTGCTCAAATGCCTCCAGATGGGGATGAACCGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001073:ENSGALT00000001607:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.324 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0010513=zf-C4=WD(100=82.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGGTCACAGCACACGTC
R:
CTTTCCGGTTCATCCCCATCTG
Band lengths:
342-1638
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]