GgaINT0000532 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:374366-374927:+
Coord C1 exon
chr8_random:374366-374479
Coord A exon
chr8_random:374480-374798
Coord C2 exon
chr8_random:374799-374927
Length
319 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGA
5' ss Score
6.99
3' ss Seq
TTTGCTTTTGTTTTTTAAATAAG
3' ss Score
-2.08
Exon sequences
Seq C1 exon
ATATTAACGAGTGTCAAGAGTCCAATTCCTGTCATCAGCATTGCATCAATACCGTAGGAAGTTTCCACTGTGGTTGCGATCCAGGATACCAGCTAAAGGGCAGAAAATGCATAG
Seq A exon
GTATGAATTAGTTTTGAAATTTCATTCCCTCTTCCTAATGGAAATAGTTAAACACTTACTTGTTACTGTACGCAACTTTATCCAAACCCTTTGTGAATGTAACTCCAACTCAGCATGACATCTTTAGTATGTATTCTCGAATTTGTAAAGCAGCACTAAAATCTAGAGGAAGAAGGATCTGAGCTGACTGATAAATGTGTATGAAATGCTTCCAAATGCATGCACGTAGTATGATCACAACTAGATTATGCTGCTCTTTAGGAATTGAGCATAAGGAGTTCATTTCCATTCCTGCTTTCTTTGCTTTTGTTTTTTAAAT
Seq C2 exon
AAGATGTAAATGAATGCAGGCAGAATGTATGCAGGCCTGATCAGCTTTGCAAAAACACCCGTGGTGGCTATAAGTGCATTGAGCTGTGTCCAAATGGAATGACCAAAGCAGAAAATGGAACTTGTATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:101
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:
PF0764510=EGF_CA=WD(100=94.9)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=93.2),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATTAACGAGTGTCAAGAGTCCA
R:
ACAAGTTCCATTTTCTGCTTTGGT
Band lengths:
238-557
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]