RnoINT0106581 @ rn6
Intron Retention
Gene
ENSRNOG00000012750 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:RGD Symbol;Acc:1563142]
Coordinates
chr3:160410757-160412982:+
Coord C1 exon
chr3:160410757-160410949
Coord A exon
chr3:160410950-160412788
Coord C2 exon
chr3:160412789-160412982
Length
1839 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
TCTCCTTGCCTCCTCTCCAGCGG
3' ss Score
9.09
Exon sequences
Seq C1 exon
ATGGACACCAGGGGCCACGGCTGCTCACTCTCCTCGCTCTATGTGGGCGATCTGCACCCCGACGTGACCGAAGCTATGCTCTATGAGATGTTCTCCCCCATCGGCACTATTCTTTCCATCCGTGTGTGTCGGGACGTGGCCACCCGGCGCTCTCTGGGCTATGCCTATATCAACTTCCAGCAGCCTGCTGACG
Seq A exon
GTGAGCCCCAGAGAAGAGAAAAGTTTGCTTTTAACATTCTTGGGCAAAATACTTTCCTTTTGATAACTACCATCCTGAACTGGAAAGTTTTCCTTCAAACGAACTATTATTGGCTCAGTAATAGTGATTATCTATCTTTTAGGTAGAAATGGGCCTGTAGCTAATTATGGGTATTTTATATTACAGATCGTAGCCAGAGAAGATTGGGCAGCCTGTGTTTCCATCGTCTTTATCATAGTTAGGGAAAATGAGGCCCAGAGACAGGGAGTTGGAAGGTAGGCATTCAGTCGTTGAAGGGAGAATTGACAATTACTGCTGGGCCTGCTGGTTGTTGCTAAGTGGCTTTGAGATTAAGCAGAGCTGGGTTAGGAATCCAGGATCTGTGTGACATCAGGCAAGTGGCTCAACCACTCTGAGCTCAGTTGGCTGTGTGGAAGGAAACTGAGGTTCTGCCTCTCTTCAAGAATGGTTATATATGAGATTGACAGCACCTGGGAGGAAGCTACCCAAAGCCTTGCAGGTGTAGGGTGGGGAGGAGGCCTTGGGTTGCTGCCTTCCAGTGTAGCCTGACCTGAGGTCTACACCAGGTGCCTTGCCTTTCTGATTCCGGAAGAGCCGCCTCCTGTAGGCTTTGACAGCCACCGTCAGGGTGAAAGCATTGATTAGTAATTGTCAGCTGAGCATGTCTGGTCTTCTGCTGAAAACGGAGGACACAGGTTAGGAACCGTGGTTTTGCTGAGGCTATGGCACTGGGCAGGACCACCCTTGGTGAGAGGCCAAGGCTTGTTTCTCAGTATCACGAAGAATGGGAAACCGGAGTGTGAGGTACCATTAGGGACACTGGATGTACTCTTAAGTGACAGTGCATGAACCACTCCAGAGATGTAACCAAGAACTGTCCTCCCCCACTTACTGGGGAAGCCATGGCAAGAACATGAATTCGAGGCTAGCATGGGCTGCATATTGAGATCCTGTCTCAAGGTGAAGTAGTTCAGGCCTCAGTGTGAGTCAGGAGCTTTGCTGAGTCCAGGATGTTCAGGCCCTCCACTACACCCCACTTCTGCCTATGCCTGCTGAAAGGCAAATCTCCTGACTGAAGCAGGACCTGACCATCAGGGCCCAGTCCGTAGATGGGAGATCTGAACTGTGGGGATTCTGACTGGGTCTGTTAGCAGTCGGTGGAAAGTACAGATGTCTGCGGCCTGCTCCACTGCATCCTGTTTGCCTCTTCTGTGCCTCTGAAGCTAGCAGGGTCCCTGAAGCAGGTGGCACATTATCTGCAAGGAATAGGCTGTCCAAGTAGAAGGGTGCTGGGTGGAGGCCATTGCTTCTGCACGTGCCACCATTTACCAAACATCTGTTCCCTGCAGAGTGCAAAATCTAAGTACCATTCGTTGCATGTTTTACTTATCAACCTGCTTGACAGGCCAGCAATAGGTGACATTGTTTCATTTAGGCGTAGGAAGGAAGGTGCCGTCACCACCTCCTCACTTCCCAGGGGAACTAGTGAGGGGGGGGGGGGTCACTTCCCTTCACTCACGTGCTCACCCATGCAAGTGTGTCCAAGGCTGGAAGACCCAGGCTCTGCCTTTGCAAGCCTCACTCTTCCCATCTGTACGATGGGGATCCTTGCTACTTGCTGAGGGTTGATCTTTCCGCAACGGTGTGAGGAGTACCGTGTACAACAATTCCCTCAGCCTAATCCACCATTCTCCCAGGCTCACACCTCAAGTAAGGCCCAGACCATGGCTTTCCTTTCCCCCATTCGAGAAGGACTTGAAGATTCAGGGTCACAAATGTCACCTAACTTGCCCCTTTCTCTCCTTGCCTCCTCTCCAG
Seq C2 exon
CGGAGCGGGCACTGGACACGATGAACTTTGAGATGATCAAAGGCCAGCCCATCCGAATCATGTGGTCCCACAGAGACCCAGGCCTTCGAAGGTCCGGTATGGGCAACATCTTTATCAAAAACTTGGAGAATTCCATTGACAACAAGGCTCTGTATGACACCTTCTCCACCTTTGGGAGCATCCTGTCTTCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012750:ENSRNOT00000055172:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(73.2=80.0)
A:
NA
C2:
PF0007617=RRM_1=PD(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
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:
ACTCTCCTCGCTCTATGTGGG
R:
GACAGGATGCTCCCAAAGGTG
Band lengths:
354-2193
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]