GgaINT0000536 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:381753-382637:+
Coord C1 exon
chr8_random:381753-381872
Coord A exon
chr8_random:381873-382510
Coord C2 exon
chr8_random:382511-382637
Length
638 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
ACCTGTTTTCTTTCCCACAGACA
3' ss Score
13.02
Exon sequences
Seq C1 exon
ACATTGATGAATGTGAAGCCAGAGATACATGCCAGCACGAGTGCAGGAACACCCTGGGAAGTTACCAGTGTGCTTGTCCCTCTGGTTATCATCTTATGCCCAACGGCAAAACCTGCCAAG
Seq A exon
GTACAGAAATCTCTTTGAGAGTGCACAAATGTGTTTGTAAGTAAATGAGTTACAAATCACATTTGGCATTTGTATTAAGCACTTGCTGAATTTCCTTTCTGAGATATAGCATTCAATATGTCAAGTTTTTATATTTTACATTTCAACATTTAATAAAACATCAGCAAATTAGACAAATGCAACTTATTATTCTCTGATGTTTCCTCACATGCACATTTAACTCCACACAAGTACACAGCAGCTCTGTGGTCAAACCCAACTCTTTATCTGTTCTGGTCAAAAAAAAAAAAAAAAAAAACCTGTTAGATTTTTGATGCACCAAAAACCCCAACCAATTAACCTCTGTTGAAAAGATAACTATAGGTGATGTTGCATAGTGGTTGTAGGGCAGCTAGCACAAAACACGGTCCTACACAGAAATGAAATGCCCAAATCAATAAATGTAAGTCATTTGAACTAGTAGCTTCAGTACCTCTGGGAGCAAGGCAGGATTCTGAAGAGTTCTGTTCTCACCTGTGTGTAGAGGCACCCGCACTCTCTCTGCCATCCACTCACTTTGCTGATCCAGCTACTTCTTATCTCTCTTAAATTCCTCCCAGAACCAGCTATTGATTGTGTACCTGTTTTCTTTCCCACAG
Seq C2 exon
ACATTGATGAGTGCCTCAAGCAGGACACTGGCTGTGGAGCAAGCCAGATGTGCTTCAACATGAGAGGGAGCTACCAATGCATAGAGACATCTTGCCCACCAAACTATCAGCGGGAGCCTCATTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:105
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:
PF126622=cEGF=PD(16.7=7.3),PF126622=cEGF=PU(83.3=48.8)
A:
NA
C2:
PF126622=cEGF=PD(12.5=7.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATTGATGAATGTGAAGCCAGAGA
R:
CCAGAATGAGGCTCCCGCT
Band lengths:
246-884
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]