GgaALTD0001983-2/4 @ galGal3
Alternative 5'ss
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:372169-373641:+
Coord C1 exon
chr8_random:372169-372231
Coord A exon
chr8_random:372232-372529
Coord C2 exon
chr8_random:373522-373641
Length
298 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGCA
5' ss Score
-1.95
3' ss Seq
AAAATGTTTCCTTCCTGCAGATG
3' ss Score
11.17
Exon sequences
Seq C1 exon
GAGATCGTAACAACCAGTGTCCTGCTGGGTTTGAGTTGAACTCATCTGGGCCTTACTGTACAG
Seq A exon
GTAATACGATGCAACAAGTTTAATATGTAGTCGGGCAGCAGCATCTTCATCCCTTCTGTTCAGAGCTCCTGAGCATGCAGGGCACACTCCAGGAAGTGGAAGCTGCCACCAATGGACAGATGTGGGCCCAGAACACAGAAGCAGGTCCCAGGCAGCCTTCCATCAGCATTGTGATGCGAAGTGGGACTGCTGAGCTGCTGTGCTCACTGAGCCTTCAGACCAGTGGAGCACTCTGAGAGGGGAGGGAGGAGGGCTGGGGGCCTAGAGAGCAGCCCACTGAAAACCAGCTGTTGCTTGG
Seq C2 exon
ATGAAGATGAATGTGCTGTGCGAAATCCCTGTTCCCACACCTGCCACAATGCTGTAGGAACCTACCACTGCTCCTGTCCAAAGGGCCTCACCATTGCTGCAGATGGCAGAATGTGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141-113-134,114-134,115-134,116-134-2/4
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF126622=cEGF=PU(80.0=72.7),PF146701=FXa_inhibition=PU(4.9=9.1)
A:
NA
C2:
PF126622=cEGF=PD(15.0=7.3),PF146701=FXa_inhibition=PD(92.7=92.7),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion 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:
CGTAACAACCAGTGTCCTGCT
R:
CCATCTGCAGCAATGGTGAGG
Band lengths:
164-462
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]