BtaALTD0005429-3/3 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000016779 | CLIP1
Description
CAP-GLY domain containing linker protein 1 [Source:HGNC Symbol;Acc:HGNC:10461]
Coordinates
chr17:55309212-55312261:+
Coord C1 exon
chr17:55309212-55309928
Coord A exon
chr17:55309929-55310156
Coord C2 exon
chr17:55312145-55312261
Length
228 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGT
5' ss Score
7.81
3' ss Seq
CATGTAACTCTGTCTGGTAGGCT
3' ss Score
6.02
Exon sequences
Seq C1 exon
AGCATTTTGGAGCCCGGGAAGAAATGCATCAGAAGGAGTTAAAGGTTTTGCAGGCCGCCACAGAGAAGCTTTCCAAAGAGAATGAGTCCCTGAAAAGCAAGCTCGACCACGCCAACAAGGAGAATTCAGACGTGATCGCCCTGTGGAAGTCTAAGCTGGAGACAGCCATCGCGTCCCACCAGCAGGCCATGGAGGAGCTGAAGGTGTCCTTCAGCAAGGGGGTCGGCACCGAGACAGCCGAATTCGCCGAGTTAAAAACGCAGATAGAGAAAATGAGACTGGACTACCAGCAGGAAATAGAAAATCTGCAGAACAAGCAAGACTCAGAAAGGTCTGCTCACACGAAAGAGCTCGAAGCCCTAAGGGCTAAGCTGATGCAGGTCATTAAAGAGAAGGAGAACAGTCTGGAAGCCATCCAGTCGAAGTTGGACAAAGCGGAAGAGCAGCACCTAGTGGAAATGGAGGACACCTTAAACAAACTGCAGGAAGCCGAGCTAAAG
Seq A exon
GTAAAGGAGCTAGAGGTGCTACAAGCCAAATGCAATGAGCAAACCAAGGTTATTGATCATTTTACATCACAGCTCAAGGCTGCCGAAGAAAAGCTCTCAGACCTTGATGCGCTTCAGAAAGCCAGCTCCGAAGGTAAATTGGAAATCGAGAACCTCAGACAGCAGCTTGAGGCAGCTGAGAAACAGATTAAAAACTTAGAGATTGAAAAGGATGCTGAAAGCAGCAAG
Seq C2 exon
GCTAGTAGCATCACCAAAGAGCTGCAGGGAAAAGAGCTAATGCTTAATAACCTTCAGGAAAACTTGAGTGAAGTCAGTCAAGTGAAAGAGGCTTTGGAAAAAGAACTGCAGACTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016779-18-14,19-14,21-14-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.343 A=NA C2=0.231
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGCCGAGTTAAAAACGCAGA
R:
GCTCTTTTCCCTGCAGCTCTT
Band lengths:
294-522
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development