RnoINT0106603 @ rn6
Intron Retention
Gene
ENSRNOG00000015642 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:RGD Symbol;Acc:1305015]
Coordinates
chr5:140986996-140987981:+
Coord C1 exon
chr5:140986996-140987090
Coord A exon
chr5:140987091-140987843
Coord C2 exon
chr5:140987844-140987981
Length
753 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
ACGTACATCTTCTCTCTCAGGCT
3' ss Score
8.28
Exon sequences
Seq C1 exon
GTAAGACCTTAAGTGTCAAGGTGATGAGAGACTGCAGTGGGAAGTCCAAAGGCTTCGGCTTCGTGAGCTATGAGAAACATGAGGATGCCAATAAG
Seq A exon
GTAAGAGCGCTGTGAGGGTCGAGAAGAAACTGGGCGGCACCTAGTGCAAAGTAGAGTAGCTAGAGGGGGCTCAGTGGGTGTGCAGCTCTGCCCAGCATCCAGTTAATGATCTGTTAACTGTCAGTTCAGATACTGATGGAAGATTGGGGCAGGTGGTTGTCCCCATTCTTGGGTAGAGAAACTGAATCCTTTAGGTAGGGCAATGTGCTGGACCCTTAACCTACAGAGGGGCCTGAAAAGTTGAGCGTTATCAGATCATCAGTCAAGACTCACCAGCCCTTGCCTAATTTTTATACAGATACTGTGTTTAGAGACCACCACTCCCCACCACCGTACACACATACCCTTTACACCCTCTGCACTCAAATCTTTCCCAGGCCTGCTGCTTGGTGCCGGTCTGGGGACAGGCAGTGCAATAGTAGAGCAGAGGAAATCCAGACGGGTTGTTTCCATCTGTCCTGGGGCCTGTCTCTACAACTCTGCCACACTCCTTGAGAATGAAGGTGTTTTTGAAGATGCTGAAGCTAGGGGTGGGAATTAAGGGAAAAAAGATGTCTGCATCAGTAATGACCAGTAACTCATTTAGGTGCTGACTCCACTTCCCTCCTGAGTGGGGTTATAGTGTAGCAGACTTCAGTGTCCATCAGTCCATCGAGAAGCATTTTCCTTGGTGTGCTGGGCTCTGCTACAGAAGATGGCCAAGTCTCTGTGTTACGTATGTCTTCAATTAAAGACGTACATCTTCTCTCTCAG
Seq C2 exon
GCTGTGGAAGAAATGAATGGAAAAGAAATGAGTGGGAAATCCATATTTGTAGGCCGTGCTCAGAAAAAAGTAGAACGTCAGGCGGAGTTAAAACGGAAATTCGAACAGCTGAAGCAGGAGAGGATTAGTCGGTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015642:ENSRNOT00000056592:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.031 A=NA C2=0.109
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:
AGACCTTAAGTGTCAAGGTGATGA
R:
CTGGTACCGACTAATCCTCTCCT
Band lengths:
230-983
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]