RnoINT0106608 @ rn6
Intron Retention
Gene
ENSRNOG00000029749 | Pabpc4l
Description
poly(A) binding protein, cytoplasmic 4-like [Source:RGD Symbol;Acc:1559517]
Coordinates
chr2:130656212-130658202:-
Coord C1 exon
chr2:130658074-130658202
Coord A exon
chr2:130657541-130658073
Coord C2 exon
chr2:130656212-130657540
Length
533 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
CTGTACTTCCACTCTTGCAGGAA
3' ss Score
10
Exon sequences
Seq C1 exon
GCCCAGCAGAGGAGGCTGGGGAGCAAGCTAGAGGGGCGGGGGAGGAACACTGTTCCCCAAAAAGTTCGAAAGAGTAAACAGTGTTAGCCAGCGAGCTCCGGGTTCCTGCCGCCTGCAGTCCGGAACCTG
Seq A exon
GTGAGCTTCAGTCTTCAGCCAGTCTCCTTCCTGGCGCCTCTGGCCGCGGGGTACGGGGTGGGTGGCCAGGGACGCGCGGCCCAGGCGCGCGCTCTCAGGCGCGGGGCGGGCGGGATGGGTCGGGCTCCCTGCGCGGGACGGGGGCCTCCAGTCCTGGGCCTGGGCTGCATGACCCCACCGCGCTCCAGGCTGGTCTGGGGGTGGCAGGATAAGCCAAGGGGAACATAAGGCCTGTTTGTGCTGGGAAAGCAGCCACCAGCTGCTGGGATGGAGGCAGATGGAGGGCCTGTTCTGGCCAGCCACTTGTAAGTTGTTGCTGAGTTGGAAGGGAAGGAAAGTCTGAGGCTGAGAGCTGAGGGCAGTTAGCCAACTACCAGGGTTTCTACAACTACTTTGCTTTCTGCCTTTCTCTCTTCATGAGAGGTGTTGCCTGGCTCAGGGAAAGTGCAACTGACCCTGCAGCTGGTCCCCTAAGTGGTCCTCTTAGGCCACTGTGCAGGTCCTGAGTTGTGACTGTACTTCCACTCTTGCAG
Seq C2 exon
GAAGACACATCATTGGGAGCTGCCCGGCCTAATCTTGTAGTGTTGGGGTTAAAAAAAGAAACAATCCAAACAAGCCAAGAACAAAAACATGAGTGTGGAAACTAAGTACCGTGCGGCTTCCCTGTATGTGGGTGACCTCCACGAAGATGTCACGGAGGACCTTCTGTTCAGGAAGTTCAACACAGTAGGACCTGTGTTGTCCATCCGAATCTGCAGGGACCTGATTTCCCATCGTTCACTAGGCTACGGCTATGTCAATTTTCTCCAGGTGGGTGATGCCCAGAAGGCCCTAGAAACTATGAACTTTGACTTGATCAAAGGTAAATCCATCCGTCTCATGTGGTCTCAACGGGATGCTTGCCTAAGGAAGTCGGGAATCGGGAATGTGTTTATCAAGAATCTGGACAAATCCATTGACAACAAAACCTTGTATGAACACTTCTCACCTTTCGGAAAGATCATGTCCTCCAAGGTGATGACTGATGAAGAAGGCTCCAAGGGTTACGGCTTCGTGCACTACCAGGACCAGAGAGCAGCTGACAGGGCCATTGAGGAGATGAATGGGAAGCTGCTGAGGGACAGCACTTTGTTCGTGGCCAGATTCAAAAGCCGTAAGGATCGGGAGGCTGAGCTCAGAGAGAAACCCGCCGAATTCACTAATGTGTATATCAAAAATTTTGGGGATGACATGGACGATGAGAGCCTCAGGTCAGTTTTCAGCAAATACGGCCAAACTTTGAGCGTTAAGGTGATGAAAGATGCCTCTGGCAAGTCCAAACGCTTTGGATTTGTGAGCTTTGATAGCCACAAGGCTGCGAAAAACGCAGTTGAGGACATGAATGGGCGGGACATAAACGGGCAGACAATTTTTGTAGGCAGAGCCCAGAAGAAGGTGGAAAGACAGGCGGAGTTAAAGGAAATGTTTGAGCAAATGAAAAAGGAAAGAATCCGTGCCCGCCAGGCAGCTAAGCTCTACATTAAGAACCTGGATGACACCATCGATGATGAAACACTGCGCAAGGAATTTTCTGTCTTTGGGTCCATTTGCAGAGTTAAAGTGATGCAGGAAGCAGGGCAGAGCAAAGGGTTTGGCTTGATCTGCTTCTTCTCCCCGGAGGCAGCTGCTAAAGCAATGGCTGAGATGAATGGCCGCATCCTGGGCTCCAAACCCCTCAACATTGCACTGGGTCAGAAGCACTGAACACAAAATGATCCTACCTCACAATCTGAGCAGCAGCTAGGAGAACAATCCTGCTCTCCATCTATCAGGTGCTAGAAGGAAGGGTAATCTTCAAAACCCCAGTGGCTGCTTAATTCATTGCAATCGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029749:ENSRNOT00000017012:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0007617=RRM_1=WD(100=19.1),PF0007617=RRM_1=WD(100=18.6),PF0007617=RRM_1=WD(100=18.9),PF0172511=Ham1p_like=WD(100=37.7),PF0007617=RRM_1=WD(100=18.6)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGGGAGCAAGCTAGAGGG
R:
GGAAATCAGGTCCCTGCAGAT
Band lengths:
343-876
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]