BtaINT0106828 @ 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
chr3:107089801-107090691:+
Coord C1 exon
chr3:107089801-107089895
Coord A exon
chr3:107089896-107090553
Coord C2 exon
chr3:107090554-107090691
Length
658 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
GTCATGTATTTCCTCTTCAGGCT
3' ss Score
8.4
Exon sequences
Seq C1 exon
GTAAGACCCTAAGTGTCAAGGTGATGAGAGATCCCAGTGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTACGAAAAACACGAGGATGCCAATAAG
Seq A exon
GTGAGAGTAATATGAGGGTTGGGGAAAATTTGTAGGGAGTGGCCCCAGCGTGTGGGCAGGGTCTTACCATCACATAGGGTGGAGCTGGCATTCCCTGAGAATCTAGTAGTTATGTGCAGTCTCTGTGCTCTGGAGTTATCTTCCCGAGGCATTTCACATAACTTTTCAAAGCATTTGGCATGTGCCTGTCACCTCAGCTCTTCAGGCCTGTAGGTTGAAAGTGTAAGGCAGGGGTTTGTTCCCACGTGTAGGTGAGGGAACCAAGAGCCCAGAGTCGCTGATCTGTGAGCAGTAGCCACTTCTGGGGAAAGCGTTGTGCTAGGCCCTCAACACTCAGTATCACTCAGTATCCTCGAAAGAACCCAAGAAATGTAGTGACAGCCAAATTATCAGCCTAGGCTCGTGTCTGCTATGCTTGTATTTATACAGCTGTACGATTTTTTCACTGTATTATCTCGACCAATGACCTATTTAAATATTAACCCTATTTTACTGATGAGAAGGTTTGGATTGGCTTAGCTGACTTCAGAGGGAAGTTAGTTTTTAGCCCTATAGGGAAGATTTCTTTCTCTCAGAATATTTGGTGGGATTTAACATACCTACAGAGCAAGGCCCCTGCCTCTGCATCTTGGTTTAAAGTCATGTATTTCCTCTTCAG
Seq C2 exon
GCTGTGGAAGAGATGAATGGAAAAGAAATCACTGGGAAGGTCATTTTCGTTGGCCGTGCACAAAAGAAAGTGGAGCGGCAGGCCGAGTTAAAGCGAAAATTTGAACAGCTGAAGCAGGAGAGGATTAGTCGCTATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017125:ENSBTAT00000022761:5
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=0.087
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(44.3=100)
A:
NA
C2:
PF0007617=RRM_1=PD(21.4=32.6)
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:
GTAAGACCCTAAGTGTCAAGGTGA
R:
ATAGCGACTAATCCTCTCCTGCT
Band lengths:
230-888
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]