HsaINT0119444 @ hg19
Intron Retention
Gene
ENSG00000174740 | PABPC5
Description
poly(A) binding protein, cytoplasmic 5 [Source:HGNC Symbol;Acc:13629]
Coordinates
chrX:90689597-90693583:+
Coord C1 exon
chrX:90689597-90689893
Coord A exon
chrX:90689894-90690433
Coord C2 exon
chrX:90690434-90693583
Length
540 bp
Sequences
Splice sites
5' ss Seq
TCGGTCCGT
5' ss Score
3.06
3' ss Seq
TCTGAACTTCATTTTCTCAGCCT
3' ss Score
3.93
Exon sequences
Seq C1 exon
AGGAAGCGGGAAGTTACTTAGCACGGTTCCGGGTTTCTCGCGCCCCGCCTGTCCCCCCTCCCTATCACTGCTACTGGCTCTTGGTCCCTCCGTTGGACTGTCCTGCGGAGAGAAACCCCAGCCCATCGGTCTGCGCTGGGACCGCCCGCCGCGCATCTGCCCTTCTTCGCTGACTCCGCCCCGCATCTGGCCAGACCCGCCTCGCGTCAGAGCTGACCCACTCACTGCGCGTTTGCCAGTCAGTCTCTCCGGACCTGCCTCGAGCCTCAGGCTGCTGAAATCACCGCGCCTCACTCG
Seq A exon
GTCCGTACCCAGTGGGCATCTTGGGTATCTGGGCGGTCTTCGATCCCCCGCGCGTGTGTCTGTCTGTCTGTCTCTGTGTCCTATCCGCTGCCTGCAGCCTGCCTGCCGGTCTTATCGCACCAAGTGTCTGGTGTACCCTTTCGCAGACGCTGAGTGCGGAGAGGCCTTAGCGAAAGGCTAGCCAGCCCGAGACTGGCCAGGCAGCCGGCGGAGGAATACGCGCTCGGTCCCTGCCCTTGTTGATATCATTTTAAACCAACAGGAGCTCTAGGCCTATATTTATGCAGAAAGCGGGTCGGGAGGCCTCTGTCTGCAATGCTAGTTGTGGGGAACCAGCCAGCTGCTTGGTGGCTTCTCACAATTTCACGGGGACAGGAAAATTACGTTTCTGGTACTGGCTTTTGAAACTGATTTTAAATCTGAACGGGTGACAATTTTAAGTCCCCGCAGGGAGAATAGATTCGTATTTGGGGCGCCTTTTTGTCTGATGTGTTTGTTCTGAGCCTGCTGACCAGCTGTTTCTGAACTTCATTTTCTCAG
Seq C2 exon
CCTCGACAGTGATTCTGAGTCTGCTTTTAGCTTCCTTTTGCCTGCCTTGGCTTTTTCTGTTCGTGAACAGCTGTTTGGCCCATAGCTTAGAGAAAGCAGCCTTTTTTCTCTTCAAAGAGAACCTCCTCCCAGTGCTCAGAGAGATGGGGAGCGGGGAGCCTAATCCTGCTGGCAAGAAAAAGAAGTATCTCAAGGCCGCTCTGTACGTGGGTGACTTGGACCCAGATGTCACCGAGGACATGCTCTATAAGAAGTTCAGGCCTGCTGGCCCTCTGCGATTCACCCGAATCTGCCGTGATCCGGTGACCCGCAGCCCCCTGGGCTATGGGTATGTTAACTTCCGCTTTCCCGCGGATGCAGAGTGGGCCTTGAACACCATGAATTTTGATTTGATTAATGGAAAACCATTCCGCCTTATGTGGTCTCAGCCAGATGACCGCTTAAGAAAGTCTGGAGTGGGAAATATATTCATCAAAAACCTGGACAAATCCATAGACAATAGGGCCCTGTTTTACTTATTTTCTGCTTTTGGGAACATTCTGTCCTGCAAAGTCGTATGCGATGACAACGGCTCTAAGGGTTATGCCTATGTTCACTTTGACAGCCTGGCCGCTGCCAATAGAGCCATCTGGCACATGAATGGAGTGCGGCTCAACAACCGCCAGGTGTATGTTGGCAGATTCAAATTCCCAGAAGAGCGGGCGGCTGAGGTCAGAACCAGGGATAGAGCAACTTTCACCAATGTTTTCGTTAAAAACATTGGAGACGACATAGATGACGAAAAACTGAAGGAACTTTTCTGTGAATATGGGCCAACTGAGAGTGTTAAAGTAATAAGAGATGCCAGTGGGAAATCTAAAGGCTTTGGATTTGTGAGATATGAGACACACGAGGCTGCCCAAAAGGCTGTGCTAGACTTGCATGGAAAGTCCATCGATGGAAAAGTCCTCTATGTAGGGCGAGCACAGAAGAAAATTGAACGCCTGGCTGAGTTGAGGCGGAGATTTGAACGGCTGAGGTTAAAAGAAAAAAGTCGGCCCCCAGGGGTGCCTATCTATATTAAGAACTTGGATGAGACAATCAATGATGAAAAACTGAAGGAGGAATTTTCTTCCTTTGGGTCAATTAGTCGGGCCAAAGTGATGATGGAAGTGGGGCAAGGCAAAGGATTTGGTGTGGTCTGCTTTTCCTCTTTTGAAGAGGCTACCAAAGCAGTGGATGAGATGAATGGCCGCATAGTGGGCTCCAAGCCCCTGCATGTCACCCTGGGCCAGGCCAGGCGCAGGTGCTGAGAATAAGAATGCTCAGTTTGTTTCAGCCTTAGTTGGTGCCTCCTTAGTTTGGGCTCCTTTGTGATAAGGGGTTATTTTATGCTAATTCACAAGTTTTTTTTTGAAGTGAATTCTTTTGAAAAAAAAATGCAAAACTAGAAAACTTTATTCATTTTAGAATAGAACATAATTTCTAACTGTAAAATTGTCATTTTGTACTTTTTTTGATGTAATATCCTTAGAAATCTGTAGAATAAAGTGTATTCCTCCACTTTTTTTTCCTGAACAGTCAAGGTGAGGCAATTGATTGAGTATATTTCCCTTCTTATTTCAGTAATACTCTATTTTTTTTCATGAAAATGTCAACATGGTTCTTCTGAATCTATCACAGTGAAAAGTTCTAACTTGTTTTTGAGAAGTCAGTACAGCAGGGGAAAACATATGTGATGCAATTAACATCTGCATAATTTCACTTAAAATTATTATGCAAAAATGAATGTTTTTTCAAAAAATGTGAAATGTATTTTATTTTCTTTATTTGTATTCTTGTTTCATTTTTTAATATGTTGTGAACATGCTACAGATTTGATAGTACTTTTGACTAAATGTTGGGAGTGGTCGTATTAACTTCTTGCCCAAAGAAGTAAGCATATTGGTGTTTTCTCAATTAGTCACTGAGAAAATTAACACTTTAGGCAGTGGCTATTTAAAGTAGGAATTGCATCTTAAAAACCTTTCCTAAGAGATTTGGTATGTGAGGATACTTTCAGTACCACTCCTACCATTCATTTTTCTAAATTCCTTAGTACATATACTTGGATCATGTTAAATTAACAAGAAAGATGAATAACTGCGCTGAATTGCCTTTACCTATAAATAATTTAATATTTTACCTTCGGGTTTTATCAACTGTCAATATAAAAGGCAGTACTCCACAGAATGATGTTGAAAAACTTCTTCGAAGAACACCTTCTATTAAACTTGTTATCTCTTGTAAATTATTGTGTGTGTCCTTTTGATAATATTCACAGGTGTTTCAAAGGTAAGGAATAGGTTGTCTCTTGGATTAAGTCATATGCCTCCAGCCATTATATGAGAACTGTGAAACCAATATGGTTTTCTTTATGTCTTGGCTGCTTGAAAATTAAAAAAAAAAAAGGTTTGTTCAATATTGCCGTTACATTTATTAGCCTGTAATTTCTAAATTGGAGATTCTCTACATTTCACTTGCAGTTTCCTGTTCTCCTCATTGCCTGCCTTCCATTCATATTACACTTATTTTTCTATTTTTTGTATTACCTTTTTAAAAATATATACCAGTTCAAGTCCTTTTAGGAAGAAGAAAATACCTAATTTATGTAAAATTTAAATAATTACTTTTTTATAATATGATTCACTTATGCCACAGATTCAACATTAGAATATGTTTTATCTCTACTGTCAGTTTTATTACCTTATATACAAATCTTCATTTTCATACATAGTACAATGTAAATATATAACTTTGTTAACACTTTTGTTAGCTCTTTGACCATAAAATAATGACAATAAGCTGTTTCTATGTATTTGTTTATCTACAAATTACAGGTTTATCCATTTGCAAATATTTTCAAAATGGAAATCACTGTTTATATTGATTATAAACATAAGACATGCTCATTGTAAAAAATGTACACAAGGCAGAAGGAAGTAAAATTTCCACAGTTCAGAAATACCACAATTAATATTTTCAATGTGTAAATATCTTTTCATAATTTTTCCTACGTATACACAAACATTTTGACCAAAAATCCACACTATATGTACTGTTCTGTATTTTTAATTTTAAACTGAACAATAATCATCTTTTCCTGACAATAAATATCAATCTCTATCATCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000174740-PABPC5:NM_080832:1
Average complexity
IR-S
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=18.5),PF150631=TC1=WD(100=12.5),PF0007617=RRM_1=WD(100=18.0),PF0007617=RRM_1=WD(100=18.3),PF0007617=RRM_1=WD(100=18.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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:
GACTGTCCTGCGGAGAGAAAC
R:
CCATCTCTCTGAGCACTGGGA
Band lengths:
349-889
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)