GgaALTA0002620-2/2 @ galGal3
Alternative 3'ss
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:338850-339735:+
Coord C1 exon
chr8_random:338850-339009
Coord A exon
chr8_random:339611-339615
Coord C2 exon
chr8_random:339616-339735
Length
5 bp
Sequences
Splice sites
5' ss Seq
AAGGCAAGT
5' ss Score
3.24
3' ss Seq
CTTTATTACCTTCCTTGTAGAGT
3' ss Score
8.5
Exon sequences
Seq C1 exon
TTCCTCCTAGTATTGTTGGCTCTGAAATGCCTAGAGAGGTCGGTGTCCTCTTGGGAGAAGGCATCCAGCTAGTATGCAATGCCACTGGAGTGCCAATGCCTGTTGTACAATGGCTTAAAGATGGAAAAACAGTTGCCAGTGACAACTTAGAAAGAATAAG
Seq A exon
AGTAG
Seq C2 exon
CTCCAGATGGCAGCACATTAAACATCTTCAGAGCTCTCACTTCTGATACAGGAAAATACACTTGTGTGGCGACTAATCCTGCAGGAGAAGAGGACCAGATTTTCAACTTGAGTGTATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141-75-92,75-91-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.023
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(53.9=88.9)
A:
NA
C2:
PF0767911=I-set=PD(44.9=93.0)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGTGCCAATGCCTGTTGTA
R:
TGTTTAATGTGCTGCCATCTGGA
Band lengths:
98-103
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]