BtaINT0106759 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005490 | P4HTM
Description
Bos taurus prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) (P4HTM), mRNA. [Source:RefSeq mRNA;Acc:NM_001076115]
Coordinates
chr22:51557553-51558557:-
Coord C1 exon
chr22:51558372-51558557
Coord A exon
chr22:51557644-51558371
Coord C2 exon
chr22:51557553-51557643
Length
728 bp
Sequences
Splice sites
5' ss Seq
CCGGCAAGT
5' ss Score
3.16
3' ss Seq
ACGGCCCCCCTGCCTTACAGCTA
3' ss Score
8.79
Exon sequences
Seq C1 exon
GGTGCTGCGCCTCACCCGCCTGTCACCCGAGATCGTGGAGCTCAGCGAGCCGCTTCAGGTCGTGCGGTATGGCGAGGGAGGCCACTACCATGCCCATGTGGACAGCGGGCCCGTGTACCCAGAGACCATCTGCTCCCACACCAAGCTGGTAGCCAATGAATCTGTACCCTTCGAGACCTCCTGCCG
Seq A exon
GCAAGTACTCCCACCTGGGGGTGGCTCCCAGACCCGGCACCCCCCTGACACCAGCACAGCCCTGCCCTGTGGGTGTTCCCCTTGGTATGGGGCCAGGAGAATGCTGGGCATCCTGCTTGAGAATTCCCCCCACCACATGTCTCCCCCAAGGCTGTTTATCAAGGGGCCCAAAAGGGGTGGTCGTCTGGTCTCAGCGGCCAGACCAAGGTACCCACAGACACTGCAACTTACCCCCAGATCCCTCAGGAAGGGGCAAGGCTGGACCCGATTCTTTCCGCCCCACTCCCCAGGTTGTTAATCCTGCGTGCACTGCTGGAGACGTCAGCTTGTCCTCTTGAAGCTGTGTCCCCCACTTCCCCTGCCAAGGCATGGTGGAAGGTCCTCCCTCTTCATGCCCTGGCTCAGCCCCTTCTAGTCGCAGCCAGCCGTCTGCATGATTCTGCTGCTTCTGCTAGCTCAACTTTCCCAGCAGGCCCTTAGGCATGGTCACGTAGTTTAGCTAAGTGCATGCACCTGTGATCTTGGCCACACCACAAAAACTGTGACACACAAAAAGAAACTGGGTCCATGTATGGGCTAGGGACATTTGGTACAGACCTCCCCTGTTGTCAGTGATCCCAGCCTGCCCCTCCGGCCCCTGGGAACCTGGGCAGCTTATCCTGCCCACTGGTAAGCCCCTGGGAGCATCCACAGCTGGGGACTTGCTCAACGGCCCCCCTGCCTTACAG
Seq C2 exon
CTACATGACAGTGCTGTTTTATTTGAACAACGTCACCGGTGGGGGCGAGACTGTCTTCCCTGTAGCAGACAACAGAACCTATGATGAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005490:ENSBTAT00000007217:6
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:
PF136401=2OG-FeII_Oxy_3=PU(30.1=69.8)
A:
NA
C2:
PF136401=2OG-FeII_Oxy_3=FE(20.5=100)
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:
CTCACCCGCCTGTCACCC
R:
TCATCATAGGTTCTGTTGTCTGCT
Band lengths:
263-991
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]