RnoINT0106604 @ rn6
Intron Retention
Gene
ENSRNOG00000015642 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:RGD Symbol;Acc:1305015]
Coordinates
chr5:140987844-140988910:+
Coord C1 exon
chr5:140987844-140987981
Coord A exon
chr5:140987982-140988814
Coord C2 exon
chr5:140988815-140988910
Length
833 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
AACAGTAATCCCCTCTCCAGGGA
3' ss Score
5.67
Exon sequences
Seq C1 exon
GCTGTGGAAGAAATGAATGGAAAAGAAATGAGTGGGAAATCCATATTTGTAGGCCGTGCTCAGAAAAAAGTAGAACGTCAGGCGGAGTTAAAACGGAAATTCGAACAGCTGAAGCAGGAGAGGATTAGTCGGTACCAG
Seq A exon
GTGAGGCGGCTGCCTTCTCCAGGGTGTGGTGCCAGTGGTGCTGTAGACTTCTGTGGGAAGGGGCATTCCCCTGCAAAGTCGGGTTTAAAGGCTGGCACCTGCCAAAGCATTGCCGGGTAGGGCCGGTGATACAGGCCTCTGTTCTGAAAGTGTCCACACACTGCTCTTGGCTGTGTGGGTTCATTTCCCTAAGATGCCCCTTTAGGCGCAGCAGCTGAAAGAGCCCTGTAGGGTGAGTGGTTGGCCAGAGCGCGTATGGGAAAGTGATGTGGCTGTATCCATGGCTCTAGGGCAGGAGTTTCTCACCGTGGGCTAATGTCAGTCCTGCAGGGGTGGGGATGTTTGTCCTGATTTGAGGCAGAGTTTACTATAACTCGGGGTGGCCTGGGGGAAATCATTGCATTAGGCTGACCTAGATCTCTAGCAACCCTCCTTCCTCAAAACGGGTTAGAGCCCCAACTCTGGAGCCTCTAGGTTTTGTTTTTTAAGGTAGGGTCTTGCTCTGTATCCTAGGCTGGCCTCAAACACTCAATAGTCCCTTGCCTTGGCCTCCTGAGTACAAGAAGGGTCACAGGCAAGAATTGTTTTTGGTTGGTAGGGTGGTTTTTGGTGAGACAGGGTTTGTTGTGTAGCCCTATCTGGCCTGGAACTCACTCTGTAGATCAGGCTGGCCTCAAACTCACAGATCCACCTGTCTCTGCCTCCCAAGTGCGGGATTAAAGGCATACACCAACCACTGCCTGACTTCAGGCAAGAGTTTTAACTTGACAGGTCCCCAAGTGTGTTGGGAAATAACTGTATAGAGATGTATTTAACAGTAATCCCCTCTCCAG
Seq C2 exon
GGAGTGAATCTCTACATTAAGAACTTGGATGACACCATTGACGATGAGAAGTTAAGGAAAGAGTTCTCACCCTTTGGATCAATCACCAGTGCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015642:ENSRNOT00000056592:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.109 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(21.4=32.6)
A:
NA
C2:
PF0007617=RRM_1=PU(40.6=87.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGTGGAAGAAATGAATGGAA
R:
TCGCACTGGTGATTGATCCAA
Band lengths:
232-1065
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]