BtaINT0106757 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005490 | P4HTM
Description
Bos taurus prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) (P4HTM), mRNA. [Source:RefSeq mRNA;Acc:NM_001076115]
Coordinates
chr22:51559089-51560698:-
Coord C1 exon
chr22:51560602-51560698
Coord A exon
chr22:51559252-51560601
Coord C2 exon
chr22:51559089-51559251
Length
1350 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
GGGGGGGATGCCCTGTGCAGGAG
3' ss Score
2.38
Exon sequences
Seq C1 exon
GTCCTGGCCCAGAACCGCCTGGGGAATGGACGGTGGATGACTCCAGAGACCATTCAGGAGATGTACTCTGCCATCAAGGCTGACCCTGACGGGGATG
Seq A exon
GTGAGCTCATATCTTGTCACTGTTGTGTCCCAGAGCCTCCTCCTGCCCCCAGCCAGGTGGCCCCTAGGCCCAGCTGCTAGAGTAGCTGGAGGTGAGGAGGTGAGGGGCCAGCAGTGCCCTTACCCCAGAAAGAGGCAGGAGCTAGACCCGCCCGCTCCCCCTTGGTGGCAGTCCAGAGGGCACCCTCTTGGCCTCGTCGGGCAGCATGTGGGGTACAGGAGGTATGGCTGCTGGCTGGCAGAGGGCAGAGCAGTGGAGCGGGAGTGAAGGAACAATGAGGTCAGCTTGGCATCCACTTATCCAGCCAGGCACATGGTCCCCGCCAGCTGACTGGTCTAACCAGGGCCCCCCTTGCATACCTCTTGCCTGCCTGGAGTCCTCTAACTGCCGGGGGTGGGTGTGGGCAGGAGAGCTGTCCTGGAAGCACCCTCCCCTTTGGTAATAACCCCCAGGAAGTATCTCAGGCGTAGTCATTTCCCTCATGCACAAGTTCTGCACCAGTTGAGGAAGCAGGACTTGGAAGGATGACCTTCCAACTGGTGAGCCCCGAGTGAAGAATCTGGCCCGGACCCGTGCCTGGAGAGGCACTAGGCTGCTCCCGCTCCCGCTGTGACACACTCACAGCCCTCGAGTGCCCCCACCCTCAGAGAAGCCCCAGCCAAAGCACGGGAGTGTGTCATTGGGATCAACCTTGTAGCAAAGACACCAGGCCACTCTTCCGGAACCCCTAGAGGGTAGAGCCCAGCTTTGTGGCCTGAGCAGGAACAGGGGAGAGTGTTCTCTTTGGGGAGAGTGGCCTGATTGCCTCTGCTGAGGGAGACTGTCTAGCAGGCAGGACTGGCCTGGGGTGTTCCACCCAGGATGAGACCTGAGGTCATGAGAGAACTCCTGGGGACCGGTTCCAGCTTACATCCTCCAGTGTGGAAGGCCCAGGACAAAACCCAGCACTGAACACTCTCTTTCTTCACCCTCTACAGGACCGGAGGGTGGCCACCACGCTCTACAGAGCCAGGCTGGAGGGCCAAGGGCAGTCCTTGGCCTAGGGTCTTGGCCATATGGCCTAAGCTTCCTATGGAGAGCCCGCTCTGGCCAATCTGACGGGGTTGGGCTTCATCCTTTTGGGGGCCAAATCAGGGCTTAAACTGAGGACACGAACTTCTCTGGGTCTTCCTGTAGGGCCTGATGTGACAGAAGCCAACTTCATCTGACCCGAGTCCAGGTTGGGGGACAGGTGCACATGGCCCCCCAGTGCCTGAGGCCAGGGGTAGGTAGGAAGGTGCAGCCTCCCCACTCTGCCCTCCCCACACGCGCGTGGTGGGCATTGATGGTGGGGGGGGATGCCCTGTGCAG
Seq C2 exon
GAGTGCTGAGCCTGCAGGAGTTCTCCAACATGGACCTTCGCGACTTCCACAAGTACATGAGGAGCCACAGGGCGGAGTCCAGCCAGCTGGTGCGGAACAGCCACCACACGTGGCTCTACCAGGGCGAAGGCGCCCACCACGTCATGCGCGCCATCCGCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005490:ENSBTAT00000007217:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.182 A=NA C2=0.018
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=FE(37.2=100)
A:
NA
C2:
PF134991=EF-hand_7=PD(12.8=20.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAACCGCCTGGGGAATG
R:
CTTCGCCCTGGTAGAGCCA
Band lengths:
217-1567
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]