GgaINT0027531 @ galGal3
Intron Retention
Gene
ENSGALG00000002093 | F1P0M4_CHICK
Description
NA
Coordinates
chr10:772571-773296:+
Coord C1 exon
chr10:772571-772676
Coord A exon
chr10:772677-772743
Coord C2 exon
chr10:772744-773296
Length
67 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
GACACCGCTCCATCCCCCAGGTT
3' ss Score
8.78
Exon sequences
Seq C1 exon
AGACTCGCGGCCTGAAGGACCCCGAGCAGGTGGAGAACCTGCAGGACCAGTCGCAGGTGATGCTGGGCCAGCACAACCGCTCCCACTACCCCGGGCAGCCCGTCAG
Seq A exon
GTACAGCCAGCCCCAGCCCCGGAGCTGCCGGTGACAGCGGGGTTGGTGACACCGCTCCATCCCCCAG
Seq C2 exon
GTTTGGGAAGCTGCTGCTGCTTCTGCCAGCCCTGCGCTTCCTCTCCTCCGAGCGCGTCGAGCTGCTCTTCTTCCGCCGTACCATTGGCAACACCCCCATGGAGAAGCTGCTCTGCGACATGTTCAAGAACTGACCCCCTCCCCGCTGTCACCTGGCTGCTGCTCGGTGGCTTTTGGGATACCCTGCGCTGTTTGTCCCCCTGTGCTGGCACTCTGTCACCCCCTGCTCTCCTTGGGGCGTGGATGTCCCCAGGCCAGCAGCCAAGTCCTTGGGGTGCTCCCAAGTGGTGCAGGAGGGTGGGTGGCAGGGGGACATCTCCAGGGTGGCACCGAGAGGACCAGGGTGGGCACCTCAGTGGGTGCCACTGTCCCCAACCAAACCCTGAGCACCCCCTGCACACGGTGCCAGCAGCGCCCCAACACAGGGACACGACACCAGCCTGGGGGTGGCACTGGGGGGGGGGACATGTGGGGGCAGAGCTGTGTTCTCCCATCCCAGGGGGCTTGCAGCCAGCCCCCCTATTTTGTACTCCAAATAAAGAGGGCTTTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002093:ENSGALT00000003264:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(19.0=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(19.6=80.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGAACCTGCAGGACCAGTC
R:
CTTCTCCATGGGGGTGTTGC
Band lengths:
181-248
Functional annotations
There are 1 annotated functions for this event
PMID: 33007388
NR2E3 produces a large isoform encoded in 8 exons and a shorter isoform of 7 exons. The short isoform may have a physhiological role, since intron 7 retention (MmuINT0110513, but normally as APA) for the generation of the short isoform appears to be developmentally regulated and has been identified in transcriptomic analysis at least in humans and mice. The in-frame stop codon at the very beginning of intron 7 is also evolutionary conserved in ten of the eleven vertebrate species considered, pointing to some functionality. This short isoform displays the N-terminal transactivator domain, can bind their target motifs and potentially interact with CRX through the DBD, but would lack the C-terminal domains H10 and AF2 (respectively involved in the dimerization and repression function of NR2E3), which are also highly conserved across species. Note: the short isoform is normally produced by APA, but standard IR would generate the equivalent protein.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]