GgaINT0000537 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:382511-383455:+
Coord C1 exon
chr8_random:382511-382637
Coord A exon
chr8_random:382638-383147
Coord C2 exon
chr8_random:383148-383455
Length
510 bp
Sequences
Splice sites
5' ss Seq
TGGGTATGC
5' ss Score
6.57
3' ss Seq
CATACTCTTTTTTTTCCCAGGTT
3' ss Score
9.47
Exon sequences
Seq C1 exon
ACATTGATGAGTGCCTCAAGCAGGACACTGGCTGTGGAGCAAGCCAGATGTGCTTCAACATGAGAGGGAGCTACCAATGCATAGAGACATCTTGCCCACCAAACTATCAGCGGGAGCCTCATTCTGG
Seq A exon
GTATGCTGATTTTTCACCCCTTTAGGACTGGTTTTCCCACATACCCCACACTTAACCTTTAATCATAAGAAGGAACTTTATCTAAGTTTAAGTGATATCAGTAACTCTTGTTCTTGCAAAAAAAGTAAAGCATTAAAACTGAAGTTTACAATTGGTTTACAGAGTGGCCATATTTTGTGCTTCCTGCACAATGAAACAAAATGGGTGGTTCTAGGCAGAATCTTTTTCCTAATTCAAGTGGAAATAGCTCCAGAATGGCCTTTTACTGAATGAGCTCCAGGAGGCTTTGATCCTTTCTGCTGATTCAGCATAATTCCTTTCTCAGCTGTGGGGCTAATTTTGCATCTGTTCTCCGGCTTACTTCTGTAAAGAAGCGATTGATAAAGACTGCACTGGATTAGCTCTGTTGAGAAGCCCAAAACTGCATACTGCAGCATGATAAATAGGGAGCAACTTCAGCTCATATAGCAAGTATGGGAATAGAACTTAACATACTCTTTTTTTTCCCAG
Seq C2 exon
GTTCTGTCTCAAAAACTGCCCGGCCAATGATTTGGAGTGTGCCCTGAGTACCTATGCCTTGGAATACAAATTTGTCTCCCTCCCCTTTGGCATAGCTGCTGGTCAGGACTTAATCCGGCTGGTTGCCTATACGCAAGATCAGGTTATGCATCCAAGGACAACTTTCTTAATGGCAGACGAGGAGCCAACAGTCCCATTTGCCCTGCGAGATGAGAACTTGAAAGGAGTTGTGTTCACCACCAGACCGCTGCAAGAGCCGAAGACTTACCACATGAGAGTCAGAGCCTTGTCTTACAGTGTTGATGGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:106
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF126622=cEGF=PD(12.5=7.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGAGGGAGCTACCAATGCA
R:
AGGCTCTGACTCTCATGTGGT
Band lengths:
354-864
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]