GgaALTA0002618-2/3 @ galGal3
Alternative 3'ss
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:285268-287878:+
Coord C1 exon
chr8_random:285268-285422
Coord A exon
chr8_random:287417-287599
Coord C2 exon
chr8_random:287600-287878
Length
183 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TCCTCTCTTCATCCTTCCAGCTC
3' ss Score
9.8
Exon sequences
Seq C1 exon
GCCTCTGTTCTTGGGTGATCCCAATGTTGAGCTTCTGGAGAAAGGTCAAGTTCTGCATATAAAGTCTGCTCGAATGGTTGACAAAGGTCATTACCAGTGCAGTGCCACTAATGCTGCTGGCAAACAAATTAAGGAGGTCAAGCTGATCATCCATG
Seq A exon
CTCGATGTGCCAAAGAGAAATCTACAGACACGGAAAAAAGCATCTCAAAAGCACCAGGAAAGATCAGAAGTCTGAATAACCTAAAATCTTTTATTCTTAGAACATTCTAATGTTAAAATTATTTAAAGCTGCACAGGCTTGTATACTAAGGCTTTTATGCTGTTGTTTTGTCTTTTGAAATAG
Seq C2 exon
TTCCTCCTAGTATTAAAGGAGGCAATATTACTACAGAGGTATCAGCACTTCTTAACAATCTTATAAATCTGGATTGTGAAACCAAGGGAATCCCTGTTCCTACCATTACCTGGTACAAAGAAGGACGCCGGATTATTTCCAGCCCCCAAGCTTTATATGTGGACAGAGGGCAGTTCCTGCAAATACCTCATGCCCAAGTGTCAGATTCTGCAAAGTACACCTGCCATGTGACCAATGCTGCTGGAGCTGCTGAGAAAACATATGAGGTGGATGTCTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141-37-48,37-46,37-45-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(58.1=94.3)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
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:
AGTGCAGTGCCACTAATGCTG
R:
TGGGCATGAGGTATTTGCAGG
Band lengths:
256-439
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]