BtaINT0150439 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021518 | TMPRSS4
Description
Bos taurus transmembrane protease, serine 4 (TMPRSS4), mRNA. [Source:RefSeq mRNA;Acc:NM_001101973]
Coordinates
chr15:29228237-29229955:+
Coord C1 exon
chr15:29228237-29228403
Coord A exon
chr15:29228404-29229812
Coord C2 exon
chr15:29229813-29229955
Length
1409 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGA
5' ss Score
8.72
3' ss Seq
AGTGTGTTTTCAACCTCCAGGGA
3' ss Score
8.27
Exon sequences
Seq C1 exon
GAAGCATCTCGATGTGCCCAACTGGAAGGTGAGGGCTGGCTCAGACAGATTGGGCAGCTTCCCATCCCTGCCTGTGGCCAAGATCTTCATCCTTGAGCCTAACGCCACATATCCCAGAGAGCACGACATTGCCCTCGTGAAGCTGCAGCTCCCGCTCACGTTCTCCG
Seq A exon
GTGAGAGCCGGCGCCTGGGGACAGAACTCCCATTCCGCCACTAGCTCTTTCACTAAGTGGCCTTGGGCACATCACTACTCTCAAGATCTCAGTTGGCCCATTGTTTCTGGCAAGTATATCAGCCTATTGTCATGAAAGCCATGAGGCCTCCTCGAGCTCTCAGCTGACACCTTACCCCTGCCAGATTCTTCTGATGTCTGTTTTCTATACATAGAGCACCCCAAGTGAGAATCACAGATTCATCCAATCTTGGAGTTGTGAGGGACCTAAAAGATCTCCTGGCCCATCCTCCACCCCAACCAATGCAAAAGCCTGCACAATCTCCCTGCCAAAGGGTCATTGAGCTCATTTGCTCTCCTCCAGGGACAGCAACTCATTACTGTTAAGGCAACCCATAGCATCTTTGACCAGCTCTGTTCAATGACTCAGGCTTACACTGGGTAGTATTTAGATCAGCATCTCCAATGGTTGGTTCCATAGAACACGGGTCCCTTGGGTACAAGAGGGTTCCTTTCTCAAATAAGTTTGGAAAATATTTTTATACCATAGCTCTCTTCCTGGAACACGTTAGTATATTAATGACATTAAGAGGGTTTGGGTTTTTTTAGCAATTTGTTTTGTTGTGTTTAATTCACATTTTCTTTATTTAAAATTATTTATTTGTTTTTGGCTGTGCTGGGTCTTGATTGCTGCATAGGCTTTTCTCCAGTTGTGGCAAGCAGGGGCTACTCTTCCTCGCGGTGCTCAGGCTTCTCACTACTATGGCTTCTCCTGTTGCAGAGCAAGGGCTCTAGGCACTCGGCTCCAGTAGTTGCAGCACATGGGCTCAGCAGTTGTGTCTCCTGGACTCAGTTGCTCTGTGGCATGTGGAATCTTCCTGGACCAGGGACCAAACTCATGTCTCCTGCATTGGCAGGTGGACTCTCATTCACTACACCACCAGGGAAGTCCAACACATTTTCTAAACTTATTTGACCACAGAATCTTTTTTTTTTTTCCCATGCTACTTCTATTAACATCCCATGGAACATGTGCTATGGAAACCCTGGTGTTAACCCTAACAGAGGATTAGCCACCAGGTTCTCCTGAACTTTGGGTCCCCTCTTCCTCTCTGCTCCTGGTAGGCACAATCAGGCCCATCTGCCTGCCCTTCTCTGATGAGGAGCTCACTCCAGGCACCCCACTCTGGGTCATCGGATGGGGCTTTACAGAAGAGAACGGAGGTAAGTGCCAGGCTCAGGATTACAGGACTAAGTGAGCAGCTCCCAAAAGTGATGGGAAGGAGGACCATCCTTTAGAAAAACCCATCCTGGAGGTCCAAGCACCAAGGTACCAGGAAACCCAGAGAACTGTCCTGGGCTGGGATTTGAAGGCAAGAATGGGAATGCAAGTGTGTTTTCAACCTCCAG
Seq C2 exon
GGAAGATGTCTGACATACTGCAGCAGGGATCCGTCCAGCTCATCAACAGAACTCGGTGCAATGCAGAGGATGCGTACCAGGGGGAGGTCACCAAGACGATGATGTGTGCAGGCCTCCCGGAGGGCGGCGTGGACACCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021518:ENSBTAT00000055576:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(24.9=100)
A:
NA
C2:
PF0008921=Trypsin=FE(20.9=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGCATCTCGATGTGCCCAA
R:
CGGGAGGCCTGCACACAT
Band lengths:
286-1695
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development