BtaINT0119933 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014947 | PTPN13
Description
Bos taurus protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase) (PTPN13), mRNA. [Source:RefSeq mRNA;Acc:NM_174590]
Coordinates
chr6:103442243-103443700:+
Coord C1 exon
chr6:103442243-103442338
Coord A exon
chr6:103442339-103443606
Coord C2 exon
chr6:103443607-103443700
Length
1268 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TCCTTTTCATTCACAATTAGTGA
3' ss Score
5.32
Exon sequences
Seq C1 exon
AACCAGTTCAAAGATACAAAACTTACCACAGTGATCTCTTTAGTACATCCAGTGAAAGTCCATCTATTATTTCCTCTGAATCAGATTTCAGGCAAG
Seq A exon
GTAAGAAGCATCTGAACAAGCAAAACATTCGTAAGAAACCATGATTGTGCTGTTTGATTCCACATGATTGTGCTGTTTGGCACCCTACTCCAGTACTCTTGCCTGGGAAATCCCAGGGATGGCGGAGACTGGTAGGCTGCAGTCCATGGGGTCTCAAAGAGTCGGACACGACTGAGCGACTTCACTTTCACTTTACACTTTCACGCACTGGAGAAGGAAATGGCAACCCACTCTAGTACTCTTGCCTGGAGAATTCCAGGGATGGGATCCTGGTGGGCTGCCTTCTATGGGGTCACACAGAGTCGGACACGACTGAAGCAACTTAGTAGCAGTATACCAGATACCTAGAATAGTCAAATTAATACTGTCAGAAAGTTCTTTTGTAGATGCCAGGGCGAGGAATGGGGAGCAAGTGCTTGATGGGGACAGAGTTTCAGTTTAGGAAGGTGAAAAATTTGGGCAATGTATGATGGTGAGTGTTGCAAAACAATGTGAATGTACTTAGTGCCACTCAGCTGTACAGTTAAGTATGGTTAAGAATAGTACGTTTTATATTATGTGACTTTTACCACAATTGAAAAAAAAACATTAAAAAAAGAAGCTATGATTTTTGTTCTTTCAGTAGTGTTGAGATATAAGGTGTGAAAAGAATAATTCTATATAAAAATTTTTAATTACAAAAAGCTTCCAATTACTCATTTTAACACTGTTATAGGTACGTAAGGGCTTCCCTCATAGCTCAGTTAGTAAAGAGTTGGCCTGCAGTGCAGGAGATCTGGGTTCAATTCCTTGATCAGGAAGATCCCCCGGAGAAGGAAATGGCAACCCACTCCAGTATTCTTGCCTGGAGAATCCCTTGGACAGAAGAGCCTGGCAGGCTATAGTCCATGGGGTCGCAGGAGCCAGACATGATTTAGTAACTAAAACCACCATAGGAACTTAATAGCAGTTTCATCAAACAGCAGTATAGTCATTTTCAAATGCTAAGTTGCTTCAGTTGTGTTCGACTCTTTGTGACCCCATGGCCTGCAGCCTACCAGGCTTCTCCGTCCATGGCATTCTCCAGGCAAGAATATGAGAGAACATAATTCATTGTTTTCAAAAATAAAATGACTGCCACTGAAGAGTTTAATGACATTATATCATTAATTTGATTATGTGAATATGATTTGTAAAAATTATCTTATGTGTCTTCTGAGTGCTTATGTTTTAAATAAGATTATTTCATATTTTTATGACTTGTGCTATTCCTTTTCATTCACAATTAG
Seq C2 exon
TGAGAAAAAGTGAAACTTCAAAGAGATTTGAATCCAACAGTGGTCTCCCAGGCGTAGATGAAACCCCAAGTCAAGGCCAGTCACAGAGACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014947:ENSBTAT00000055276:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.697 A=NA C2=0.969
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion 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:
CCAGTTCAAAGATACAAAACTTACCA
R:
TCTCTGTGACTGGCCTTGACT
Band lengths:
183-1451
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]