RnoINT0106575 @ rn6
Intron Retention
Gene
ENSRNOG00000008639 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:RGD Symbol;Acc:619838]
Coordinates
chr7:75414784-75416467:-
Coord C1 exon
chr7:75416328-75416467
Coord A exon
chr7:75414879-75416327
Coord C2 exon
chr7:75414784-75414878
Length
1449 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATG
5' ss Score
4.83
3' ss Seq
TTATTCAAAAAAATTTTTAGGGC
3' ss Score
5.79
Exon sequences
Seq C1 exon
GTTTGTTGGTCGATTTAAATCTCGGAAGGAACGAGAAGCAGAACTTGGAGCAAGGGCAAAGGAGTTCACCAATGTTTACATCAAGAACTTTGGAGAAGACATGGATGATGAGCGTCTTAAGGAACTCTTTGGCAAGTTTG
Seq A exon
GTAATGTGTCCAAGTTAAATCTTTATATTAAATTGTCTAAAGTTAGGGACTAGCATTTGACTAGAAGGCTTTAATACTTGGTTAGAATTAAGCTATAGTTTACTGCACAACAGTAACCTGGAAAGTAGACTGCTTTACAGTGACTAACACAAGATCATGTATGGGTGGCTGAGGAGATTTCAAGGTTTTGCCACATAATTTTAATTAGGATAATCTTAATGCAGACGTTAGTGTAAGAGGTAGGTGGATGGCTTCTGAGATCTTAGGGTTGGAGTAAACGAAGAGGAAATCAGTATTTGTAGGTGATTTAATGCTTATCATTGAACCTAAGAATGGGCTTTATTAAGTTCTCTATTAAAGCTAATATTGTAATGCTGTGTTGATTTGCCAAAGACAGGGTCTCATTTACGTAGCTCTGGCTAGCATTCAACTCAACAAGAGATGCCTCTGAGTGCTGGGATTAAAGGCATAAGACACACACACAGGGCTGAATCCTCTTTTGAGCAAGAGGAATTTTGATTATGCACAAATGTTAGTCATGCAAGATGACTCAAGTTTCTTTTGTATCTCTGTCTTACACCTGGAAGTTTTAAAATAAAAAGTGTGTGTGTGTGTGTGTGTGTGTCAGGGTAGCTCTTTGTACAAGGTTGGCCTTGGATTTACGAGATCCACCAGTTGTCTCCCAAGGGCTGAGGTTGGATTTTTTTTTTTTTTTAACTTATGTCACCTCTTGTACAGCCTGACTAGACCACTGTTGTAGTTGCTTTTCTGTTGCTAAGTGCTCAGACAAAGCTACCAAGGCAGCTTGATAGAGGAGTTTATTGGGCTTAAAATCTAAGGGTGGATCCATAGCCATCTTGGCAGGGAATGTGGTAGCAAGCAGGCCTGGCAGTGGAGCAGCAGCTGAGAGTGAGCTTGTTAGGATAACAGCCACAAAGCAGTTAGTTAACTGGAGTGGTATGGATCTTTTGAAACCTCAAAGCCCACCAATCAACTAGGGACCAAGTATTGAAATGTATACGGGTTTTGCTTATTCAGACAACCACTCCTAGTTCTTCCTGTACCAAGGTGTCACCTGCTTATGGTCTTCCCCACAAAAAGGGAAGGCAAAGCTTGTGTTTTTAGAAACTTTCAGGTAATTCCGTTCGTTATTTCCTGCCTGCAGATCTAGCCATTTATTCCCTCTACTGTTGAGAAGCAGATGACCAAAGAAGACTTTTTTAAGATCATTCTAAATCAAATTAATGATGTAAAGGGACAACTCTACTGACATAAGAATAAAATCTTTTATAAGTTTGTAAGACATCCTAAAAAATCTTAGAGTCCTTAGAAGTACATATGACCAGTAAAACCTTAGAACCAGGAGGCCTGGGATTTTTTTGTGTTATGTTAAAACATGAAATGTGTACACTAACTGGACTATTTTGAATTATTCAAAAAAATTTTTAG
Seq C2 exon
GGCCTGCCTTAAGTGTGAAAGTAATGACAGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGGCATGAAGATGCGCAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008639:ENSRNOT00000012775:4
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=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
A:
NA
C2:
PF0007617=RRM_1=FE(44.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGGTCGATTTAAATCTCGGAAGGA
R:
CATCTTCATGCCTTTCAAAGCT
Band lengths:
222-1671
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]