RnoINT0106586 @ rn6
Intron Retention
Gene
ENSRNOG00000012750 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:RGD Symbol;Acc:1563142]
Coordinates
chr3:160412789-160416945:+
Coord C1 exon
chr3:160412789-160412982
Coord A exon
chr3:160412983-160416829
Coord C2 exon
chr3:160416830-160416945
Length
3847 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
CCTTCCTCCCTGTGACCCAGGTG
3' ss Score
8.12
Exon sequences
Seq C1 exon
CGGAGCGGGCACTGGACACGATGAACTTTGAGATGATCAAAGGCCAGCCCATCCGAATCATGTGGTCCCACAGAGACCCAGGCCTTCGAAGGTCCGGTATGGGCAACATCTTTATCAAAAACTTGGAGAATTCCATTGACAACAAGGCTCTGTATGACACCTTCTCCACCTTTGGGAGCATCCTGTCTTCTAAG
Seq A exon
GTGGGTGCTCCTCCTCTGGGAAAGTCAGTTGGTGTCAAATACCTTTGTGGTAGAGGTCCAAGCAGCACCTCACTTCATGGGCTTTGTCACTTAGTCAGGAGCTAATTCATGGTTTTCTCCTCCCAGAACTGTTAGAGGTCACCCATGTGTCCAACAGCCAGCTCATGGTGTGTAATCAGCCTACCTCATGGTTGTCAGCAGTACTCGTTAGTTTATAATTCCAATATGGTGATTTGGGTTGAACTCAGCTGGACAGCATTTCTGGCCCTGGCTGGGTTCCCTAACATGCTACCTGAACCTGGCAGGAGCTCTCGGGAGACCCATGTAGACCTGGCCAGCTGTCAGTTAAAACATCTGGGATTTCCTCTGTGGGGTCGTCCATGCTCCTGCAGGCTAGCCCAGGGCTTTCTCTCAACTGCGGCAGGTCTCAGAAGACAGAAGTTCACCAGGCTACCTGAAACTTCGCCTCAGAGTCAGAACCCCTTTGCCCCTACTGTTTTCTATAGACCAGAGCTAGTAACAGCCCAATGCACATTCAAGTAAGGAGGTAGTTAATGACAAAGACAACAGAACAGAATTAAGCATATGGTGGCAGCAAAGCTGTTCATGGGGGCCACTGAAGCAATCAGCAGATACATCTTGCTTCTGGTGTCCCTTGGTCCTGGAAAGGGAACCCAAGCTACCACTGAGTCTCATGCCCCCTACCACATGTTGTTTTTAAGGTATTTCTTATACTAGAACTTAAACTCCACTTTATTCTTACTCACTGCTTGTCTCCCAGTCTTTCTTTGTATTCTTGGACACAGTGACTTTTCTCCCCCCATCGTGCCATGCAGTAAGTACTGAATGGATTATCATGGTTTGAGAAGAGTTCTGATTAGTTCTCCAACCTTCTATAGGAGGATGTTCAGGACTAGAAGCCTAACAGTAGGTCAGTGTGTGCTGAGTAGAGGACTAAAGCCTGCGGTCATGTCCTGGACGTCATAGAGGATGGCCCATCAGGTCCCCTGAGGTTTCTAGAGAGGCATAGGCAGAGGTACCATGATCTCAGTTTGAGTCTTCCCTGAGCACTAACAATACACCAGCTACCGTCCCTCAACTCTCAGCTGGGCCCTCCCACCTTCCCCGTGGAGACAGCCTGTCTCTGACTGACACCTGAGTATAGACTGTACCTGAGAAACAGAACAGCTCCTGCCCTGAGACCAGTGGAAGGAAGAAGCTAGGGTTGTGAATACATTCTTACATGCGTCAGCACTCGTCTGGTTGCCGGTGTATGTAGTCCCTCTGGATTCCTCCTCTCTACTTCCTCACCTCCACTTCTCCCTACCCTCCTCCCTCTCCCTCCCATCCCTCACCCTCTCTACCTACCTCCCTTTAAGATGCATGTCCCTAGGAGGGTTTCCGAGTTTTGCTTGAGACCACAGAGGTTTGAAGCTGTAAAATTGCTTGTCTGCAGTTCAATGTAGTAGATGGATGGAGGGTTAAGGTTAAAAGCTTTGGGTTTAATTTTTTGGATTTCGTTGTTGCTGTTTTTTTTTCTTTAAGATTTATTTATTTTATTTATAAATGGTTGTGAGCCACCATGTGGCTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCACTGGGCCATCTTTCCAGCCCAAGCTGTTGTTTTGGGTTTTCATTGTTGTCATTTTTTTTTTTTTTTTGAGACAAGGTCCTTACATAGTCCTGGCTGGCCTTGAGTTGCTATGGTTTCTCTGGCTACTCTGAAGTTCGGCTACCTCAAACTCAAAGCAGTCCCTTGCCTCAGTCTCCCAGAGCATTGTGCACCACCATGCCTGGCTTTAGTCATTGAACTAGTGGGCTTACCAGACCAACTGAAGTAAATTGAGCAGGGGAAGTCTACCCCACTTCTTCAGGCCTTGTGTCCCCTGGGCCACTGAAGACTGCATAGCAATCTTGGTGTGACACAGGAGAGAAGTCCTCATAGGCCTAAGGAACCCCTGCTGTGGGCACGGCTAGGAACAAGGCTCACAATGTGGTCCCTACCTCCACTCCTTGGCTTGGCTGGAGTTGGTAGGGCTTGTGGGAATAACTGGGAATTGGGCCCAGGGAAAAGGTTCTCATGGAGTCAGGGGCCCAGAAAGGAGGGAGCCACTAGGCCAGTCTAGAAAGATTTCTGTGGCATTTCTGTGGCATTTTGGGAAGAACACAAGCTTGATCAGAGTCGGGCCACCTAAATGCAAAGCCAGCCATGTAGCAGCAAGGCAACGTAATATATTGGGCCAGAAAGAGGATACTCAAGGCTAGTGTCCTGAGTCCAAATGCTTTCATGTCCTGTGTGCTGTCTGGTGGTTAATTACCCTGCCCCTACTTTGGCTTCCTCCGCAAGGGGCAGTGAGTGGTAGGACTCGTCTCTAGGAGTTGGGAAGTGGACTGAGCCGGGTGCCATCTCTGAAAAGGGACCTGGGACATGAAGCGTCTCAGTGAACATGCAATCATTTTGAAATTGCTATTCAATGGCTGACCTTGGAACAGTTATTTATTCTAATTTTCCCACTGGGTCTCAGAAGTTAAGAATCTCTAGGGCGGCTGGAGAGAGGGCTCAGTGGTTAGGAGCACTGACTGCTCTTTCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACGACCATCTGTGATGGGATCTGATGCCCCCTTCTGGTGTGCATGAAGACAGCTAGCCACAGTGTACTCATATAAAGAAAATAAATAAATCTTTCAAAAGAAGAAGAAGAAGAGGAGGAGGAGGAGGAAGAGGAGAGAGAGGAAGAGGATGAGGAAGAGGAGGAGGAAGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGAAATAGGGCTAAAAGCCTTCATTCAAGGTCACCAAGAGCTGAAAACTGGGGTATTTTTTGTTGTCCGCTTCTGCCCTTTCAGCTTGAGTCAGACCCATTACAGACACATGGAGTGTTCTGCTACAGAACTGATGTGTGTTTGTTGTTAGGATAATATATAGATTGGTAAAATTCAAACAATATAGAAGAAACTAAAGAATAAGGCTCTGTCCTTTCCATCCCTGGTCCCAGGAATACTCACTGTCAATGTTTTGTGAGGTGGGCACAGCTGTGGGCACAGCTGTACACACCTGTAATCCTAGCACTAGTGAGACTGTGGTAGTAGGATTTCAAGTTTGAAGATAGTCTGGGCTACAGAGCAAGATCCTGTCTCAAAAATCATCTGAACAAAAGCCAACTAAAGCAGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTCAAAACTTCCTATTTGTAGATCCCGCTTAACCCAAATGGGCATGATTTGGGCTCGTCCTTCAGTCACACATTTCAAATTACCGGAAGCCACATTATCTACCACATACTCTTGCAGACCAGGCAACTGTATTACAGCTTCTCTAGCCAGCCTCCCCTGAGATGTTTACAGTATCACGGTATCTTCAGTTTGCTGTCAGAATCAGGGGACAGCTGCTGGGTCGAAATCCCATGTCCACTTTCCCATAGGCCGTCACCTCGAACAAGCAGACTGGTCTTTCTCAAATTCCATCTCCCAGTTCTAAACTGGGGCTGTTGTGAGATTAGGTCTCAGTCTTCCCCCCGAGACCCCAGATAAAACCCCAGGGTCTGAGCTCCATCCCCAGCCTCCACATAATTGTCTTTGAGTCATCGGGAACATTCCTGTACTGTCACTATCCCTTTCTCTTTCTCTCCCTGAAGTCCCCATTGGGTGGCGTCCCTGTCCTTCCTCCCTGTGACCCAG
Seq C2 exon
GTGGTATACAATGAGCATGGATCACGGGGTTTCGGCTTTGTGCATTTTGAGACCCACGAGGCTGCCCAGAAGGCCATCAACACCATGAATGGGATGTTGCTGAATGACCGGAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012750:ENSRNOT00000055172:2
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(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
A:
NA
C2:
PF0007617=RRM_1=FE(55.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]