GgaINT0000443 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:265203-266031:+
Coord C1 exon
chr8_random:265203-265330
Coord A exon
chr8_random:265331-265917
Coord C2 exon
chr8_random:265918-266031
Length
587 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGC
5' ss Score
8.89
3' ss Seq
TCCTTGTTGTTTCTTTTTAGAGG
3' ss Score
9.98
Exon sequences
Seq C1 exon
GTATAGATTGACCCCAGAAGGCACCTTGATCATAAGACAGGCAATTCCAAAAGATGCAGGAGTTTATGGGTGCTTGGCAAGTAACTCAGCTGGGACGGAGAAACAGACGTCCATTCTTACATACATAG
Seq A exon
GTAAGCAAAAGAAATAATGAAGTGAAATTAAAAAGCAAAATATTCCGACTTCAGAGTGGTAATCTGTAGAACTGTGCAGAACATATTTGTAGAAATTTTCTGAAACTCCAGAAAAACAAAACAAAACATTCTAGAGTAGGCTTGCAAAACTGAGTAGGTCCTTGGAGAAGGAATACTTTTATTCTAACTTTCTGTTGTGTGCTTAGCCCAGGAGTCCCAGTTCAAATCGTGCCCTCTAAACACTATGCTGTATATTAACAGCAGAGTACCAAAATTCTTAATGAATGGTCTTCAGTTGGACTCTGAAGAGAGAGAAAGTCTCTTTTTACTTTCTAAATGGTCAGACTCTTCCAATTCTTTCCTTATGAGCGTGTATATTCTACGTATGGTTCAGGTATTGTGATATTCCAAGCTCTACTTTTCTTCTATTATTTTTCTATCACCTTACATGATTTTTAAGCCTGCTTGACTTTTAAGGCAAATATATCTTATTGTACAACAGAAGATTAATCTTTTATCATTTGCATCTTAAAAGTGATATACATTTTGGATGAGGAACTCATTTTTTCCTTGTTGTTTCTTTTTAG
Seq C2 exon
AGGGCCCAACAGTGACTATATTTCAAAGTGAAATTCTGGTTGCTCTTGGAGACACCACTGTTATGGAGTGTAAAACAACTGGAATCCCACATCCTCAAGTTAAATGGTTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:12
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:
PF0767911=I-set=PD(46.5=90.9)
A:
NA
C2:
PF0767911=I-set=PU(40.9=92.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTATAGATTGACCCCAGAAGGCAC
R:
AAACCATTTAACTTGAGGATGTGGGA
Band lengths:
238-825
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]