GgaINT0000505 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:351253-351709:+
Coord C1 exon
chr8_random:351253-351409
Coord A exon
chr8_random:351410-351587
Coord C2 exon
chr8_random:351588-351709
Length
178 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTTCTCTTTTCTTTGTTCAGACT
3' ss Score
8.79
Exon sequences
Seq C1 exon
TTCCTCCAACTATTGCTTCTGGACATACTAATATTACAGTTACCGTAAACATGCAGACCACTTTGCCTTGTGAAGCCACTGGAATTCCCAGGCCAGCAGTTAGCTGGAAAAAGAATGGGCATCTGCTTAGTCTTGACCAGAATCAGAATACTTACAG
Seq A exon
GTGAGGGATGTTTTCTTTTCACTGTGGGTTTAAAATGGATGGGGATTAACTTAGTGCTTTAAAAACTATTCATACATAAATGTAATTTTATATAGCCAACAGAATTTGTTGTCTGATTACCTGAGAAGAAAATGAAGTATTTCACTGGCTTTTACTTTCTTCTCTTTTCTTTGTTCAG
Seq C2 exon
ACTTCTGTCTTCAGGTTCCTTAGTAATCATTTCTCCCACTGTGGATGACACTGCTGTCTATGAGTGCTCTGTGTCAAATGATGCAGGAGAAGATCAAAGAGCAGTTGAGCTCACTGTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:74
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.262
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(55.6=94.3)
A:
NA
C2:
PF0767911=I-set=PD(43.3=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCAACTATTGCTTCTGGACA
R:
CCTGCATCATTTGACACAGAGC
Band lengths:
242-420
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]