BtaALTA0014051-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000001553 | HNRNPA1
Description
Bos taurus heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001045911]
Coordinates
chr5:25940997-25941802:-
Coord C1 exon
chr5:25941702-25941802
Coord A exon
chr5:25941149-25941152
Coord C2 exon
chr5:25940997-25941148
Length
4 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGT
5' ss Score
7.23
3' ss Seq
GTCCTCTTTTCCATTCTTAGGAA
3' ss Score
10.59
Exon sequences
Seq C1 exon
TGGACAGGGTTATGGAAACCAGGGCAGTGGCTATGGCGGGAGTGGCAGCTATGACAGCTATAACAACGGTGGAGGCGGAGGCGGCTTTGGCGGTGGTAGTG
Seq A exon
GAAG
Seq C2 exon
CAATTTTGGAGGTGGCGGAAGCTACAATGATTTTGGCAATTACAACAATCAATCTTCAAATTTTGGACCCATGAAAGGAGGAAACTTTGGAGGCAGAAGTTCTGGCCCCTATGGTGGTGGAGGCCAATACTTTGCCAAACCACGAAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001553-10-16,10-15-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.830
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF116273=HnRNPA1=WD(100=67.9)
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
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAACCAGGGCAGTGGCTATG
R:
CTTCCGCCACCTCCAAAATTG
Band lengths:
108-112
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development