BtaALTA0030109-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000047673 | THUMPD1
Description
Bos taurus THUMP domain containing 1 (THUMPD1), mRNA. [Source:RefSeq mRNA;Acc:NM_001046277]
Coordinates
chr25:18568829-18570516:-
Coord C1 exon
chr25:18570272-18570516
Coord A exon
chr25:18569004-18569006
Coord C2 exon
chr25:18568829-18569003
Length
3 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCA
5' ss Score
7.87
3' ss Seq
CCTCATTAATTTTATGCAAGCAG
3' ss Score
-1.67
Exon sequences
Seq C1 exon
ACCTCTAACCTACCATGGCGGCCCGTATACAGCAGTCTCCTCAGCCTGGCGGCGGGAAGCGTAAAGGCAAGGCTCAGTATGTGCAGGCCAAGCGGGCTCGGCGCTGGGATGGCGGTGGGCCCCGCCAGCTCGAGCCCGGGATACAGGGCATTCTCATCACCTGTAACATGAACGAGCGAAAGTGCGTGGAGGAGGCCTATAGCCTGCTCAACGAATACGGCGACGACATGTATGGACCAGAAAAG
Seq A exon
CAG
Seq C2 exon
TTTGCAGACAAGGATCAACAACCCTCTGGAAGTGAGGGAGAAGACGATGATGTGGAAGCTGCCTTGAAGAAAGAAGTTGGTGACATTAAGGCATCCACTGAGATGAGGCTAAGAAGATTCCAGTCAGTGGAGAGTGGAGCAAATAATGTAGTCTTCATCAGGACACTTGGGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047673-1-1,1-0-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.571 A=NA C2=0.407
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF087955=DUF1796=PU(62.2=86.4),PF0292612=THUMP=PU(26.5=72.9)
Main Inclusion 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:
GCGACGACATGTATGGACCAG
R:
TTCAAGGCAGCTTCCACATCA
Band lengths:
94-97
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development