BtaINT0106826 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017125 | PABPC4
Description
Bos taurus poly(A) binding protein, cytoplasmic 4 (inducible form) (PABPC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001083724]
Coordinates
chr3:107087983-107089467:+
Coord C1 exon
chr3:107087983-107088098
Coord A exon
chr3:107088099-107089327
Coord C2 exon
chr3:107089328-107089467
Length
1229 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
TTTTCATGGTTTCTTTATAGGTT
3' ss Score
10.81
Exon sequences
Seq C1 exon
GTGGTGTGTGATGAGAACGGCTCTAAGGGTTATGCCTTTGTCCACTTCGAGACCCAGGAGGCTGCCGACAAGGCCATCGAGAAGATGAACGGCATGCTCCTCAATGACCGCAAAGT
Seq A exon
GTGAGTGTCCCAGTCCGGAGCGACAGCCATCGCATGAGCCAGCCGTGGCCCCACCTCGGTATAAACTGGCACACACAAGGCGGCTACTGGTTCTCTCGGCCCAAGTGTGGCCTGCTCCTACCTCTCCACTCCAGGGCTGGTGAGTCTCCCTGCCTGAGCCATGGCAGCCCTTTTGACTCGCCAAGGTGGGCTTCCAGCCCAAGCCATGGCCTGCCTGCCGCCTCTCCCTTAGAAGCATCCGTCTGTGGGTTTTGTGAGCATTGACAACAGGGGCTGGCTGGAAGGCAGCTCTTGAGCCCACTCTGAGCAGGGGTCTTGGCCAGCAGCAGAGTGGAGAGGGCCCTGGACTGACCAGAAGCTGTGTACTAGCCATGTGACCTTGACCTTCCATGACTCAGGTCTGTCCGTGGGGTCACTCGCTAGGAGTTGATGCCAAATTGTCCCCTCCACTTGGCTAACTTATGAGTCAGTGGCCTTCAAAATACTAGGCTGGCTCCACAGTAGCACTTTAACAGTGAAAAATCTCATACCGGTGCAGAAGGCTGTTCATAATAGACCGTGTTGCTTTGGTGTGGTTACTTTAGAGTGGAGAGATGGTGATCTTAGTTAAGTCACGCAGAGAGAGAAGGGACCATACAGTAAATCTTAGTTATGACAAGCAAAAGTCTTTTCTGTCCATTGTGTTATTGAACGGACCAGGGAATGGGTTGCCTCAGTGGTCAGGTCTTCTAAAGGTATCACTAGAAAGAAATCTAAAAGATTTTTAATGTAAGGGTACCTTTTCCAGTTAACTGTAAGCAGCACCGAAACGAATACAGTGAAAAACAAAGGCTGCCTCTTGGTTCACTCCAACAATCTCATTCCTAGGATTAACCACTGTTAACAGTTTGGTTTGTATCCTTCCAGACCTTTTCTATGCATTTACATAGATGTACAGAAATGAACGTTTTAAAAACATGGTCATCAGGTTTCTTCACGAAGGCAGTGTGATGTGGTAGGAGGGGCCCTGGCCTGAGCCAGGAGCCCTGGGGCTGATCCTCGAAGGATAGTCCCGCCTCTTTCTCTTTCTGCTGGGAAGCTGGGGCATCTCTGAGCTTGCTCTCTTGGTGGTTGGAGGGGGACTCATGTTTTAACCTCTCCTGTCAGCCTTTAATCTGCATTCCTTTGGGCCCCTGGAAATCATGTTTTGTTCCTCTGAGTGATGAGTATTTTTCATGGTTTCTTTATAG
Seq C2 exon
GTTTGTGGGCAGATTCAAGTCTCGAAAAGAGCGGGAAGCCGAACTTGGAGCCAAAGCCAAGGAATTCACCAATGTTTACATCAAAAACTTTGGGGAAGAGGTTGATGATGAGAATCTGAAAGAGCTATTTAGCCAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017125:ENSBTAT00000022761:3
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:
PF0007617=RRM_1=FE(55.1=100)
A:
NA
C2:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
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:
GGTGTGTGATGAGAACGGCTC
R:
GCTAAATAGCTCTTTCAGATTCTCAT
Band lengths:
247-1476
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]