HsaINT0076954 @ hg19
Intron Retention
Gene
ENSG00000139675 | HNRNPA1L2
Description
heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]
Coordinates
chr13:53211440-53217919:+
Coord C1 exon
chr13:53211440-53211581
Coord A exon
chr13:53211582-53216540
Coord C2 exon
chr13:53216541-53217919
Length
4959 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CATCCAAATACTCTATCCAGCTT
3' ss Score
3.52
Exon sequences
Seq C1 exon
ACACATCACCTTCACTTTGGGATATGGAATTTGATAAGCAGTTAGCCACAGAATATGAACAACCCCTTGAGAATGAGATTGAAGAACTGATCCAGGGGACAAAAGAGGGGAAACTGAGAGTTCCCAATTAATAATGAAGCAG
Seq A exon
GTAAGTGTTAATTCCAGGGGTTATAAAATTCATTGATTGAGATTATTTCTGCCAGATATTCACTTTTAGAGTGTAGATACTTACATGAATTTCAAAACACTGTGTAGATATCTTCGCGGTGTCCTAAAGACAGTTAGTTGCAGCAGAGTCCATGCAATATAATAGAATTTTATGAAATTCAAAAACCAAATTTTGAATATACTTTCTTAGCTCTAACGGCGATAAAACTATAAAGAAAATGATCAACATAACGCGGTATTTCAGGAAGTCAGGGTAATTGAGTAGGGACACTCAGGGGCTTCGACAGTACTATCATTCTGTTCCTCAAGTTGGACGGCAGGTTCACAGGTGGTCATTTCATCATGCCTTTATGTTGTTTTATGTTGTATATATTATACTATATGTTATCCATATTATAATTACACATATTCTTTTGTTTGTAACAATGTTTCATAATATTTCAAGGAATGAATGGAAATGGGCACATAATGAAGATATGCAGTGCCTAGCCATCAGTAGAGTCCCAGCATTATCAGATTCTAAGATAATTCTTATACAAAAACAAGCAAACAAAGGGCATGTTATCTAGAATGAAAAGACCATCCATATTCTAATAAACTGAGACAATCAAATAGGGAATCCCTCTTTTAAGGATGGTATTTGTTATATGCTTGGAAGTGTTTTGAAGTAGAAATTGGTTGTAAATAAATCTACTCCTTGTTAATAGGAAAGTATAAGCTTGCTTTTAATGTCCCTGTTATCCCTACCAAGAAATTAAAAATCCTGGAGGTTAGTATTGCTTATGAACTCACTTACTTGCTTATTAATGACAGGTGCATTTGCCCTCTTAGGGGATGACCATGGGTATTTTAAAAGATAAGAAATTTGCTGAGAATTCCTTAAATTTTTCTAATTTTTACTAGCCAGTGAGGACATTGTCCCTTTTTTGCAGGTAGCTTTGAAAGATGATACCTCCACAGTTGAGACCATGTTGTTAAAACATCCTTCATTTAACCATTTACACATTTGGTTCTAAAGAATGTATTATCCTTAGATTCTTGGTTCTAAAGAATGTATTATCTTAAGATTCTTGTCTTACCACTATTCTTAAAATTTCTCTAAAACTTGCTGAGGTAATCAGCTTTAAATTCTATAAATACAGATAACAAAACCCTCTTAATCCTAAAGGTGCTTTTAAAGTTCATGCATTTATACATGTATGCAAATTGCCTATTAAATTGGGAAGATTTCATTCTAAGTAACCAAATCTTAAGGAGCTAAAGCTAACCTGCTTTATAAAATATATTAATTCCAGGACTAAGCAATTTCTGAAAACAGACTTATTTACTGTGCTGCTTAATATTTCCTCAAACTAGAATACAAGTGACGGTGGCAGAGGGAGGAAGTAACTCATACTAGGAAGAACAAATAGCTGCTGGAATATGCTTGTGGTTTAGAGCTTCTTTTAAAAATCCTGTCAGCTGCAAAGGAAAGGAAGGACTAATATTTTCCACGAGATCAGTAACATCTTTATGAAGATGCTCCTTTTGAATGTGGTACAGAAAGTTGGAAAACACTTAGGCATGGTATCTGGCATAGTGCCCCTTAGGGAGCACTTCACATGCAGACGGTCTGGGGCTTAGGATGGTTTGACTTAGAATTTTTTGACTTTATGATAGTTGCAAAGGCGATGCACATTCAGTAGAAAGTGAACTTTGAGTCCCCATAAAGCTATCCTGTTTTTCATGTTTAGGACATTGTTCCCATAAATTCATGAGCTATTCAACCCTTTATAATAAAAAAGAATTTGTGTTAGATGATTTTGCCCAAATGTAGGTTAATGTAAGTGTTCTGAGTACGTTTAAGGTAGGCTAGTCTAAGCTCTGATGCTCAGTAGGTTAGGTGTATTAAAGACGTTTTTACTTACGATATCTTCCCCTCCCAATAAACCCATTGTAAGTCAAGAAGCACCTGTAGAGGTCTGCCTTTACCAATTTCAGCTGCGACAAATTTAATGTTCCTGTATTGCTTTTAAATTGGAGAGCAGAAGCAGGTCTGAAACAAATACTGCAGTTAGCTTTGTGTTCTTCGCTATTTATTGAACAGTTCAGAGGGCAAGGAAGCAAAGAGAAGTGCTCTGAGTGTGTCTTTGCTTGCCAGCTCCTGAATTTTTAACAGTTCTACAGTGGCCTTCCTGTATTTTTCTCTCGTTTTGTGTGTTCTCTTCTGTTTTTGTTGACCCTGTCTCAAAAAAAAAAAAAAAAAAAAAATCAAAACTATCCCTTGGGAATACATAATGTTTGTATATGGAAACCCTCATGCCTTTCTTGCTACCTGTAGGATAAAGTCCAAAATCCTTAGCTTAACATTCAAATTTCTCCATCAAACTGGGTTCCTAGGCCAACTATTTCAGAGTTAATGTTGTTCTTGTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTGAGATAGTGTCTCGCTCTGTTACCCAGTCTAGAGTGCAATGGCACAATCTTGGCTCACTGCAACTGTCACCTCCCAGGGTTCAAGCAGTCCTCTCACTTGGCTCACTGCAACTGTCACCTCCCAGGGTTCAAGCAATCCTCTCACTTCAGCCTCCTGAGTTGCTGGGACCACAGGCCTGCACCATGCCTGGCTAATAGATGTGTGTATTTTTGTAGAAAGGGGTTTTCACCATGTTTTCCTGTCTGGTCTCCAACTCCTGGGCTCAAGGGATTCACCCCTCCTTGGCCTCCCAAAGTGGTGGGATTACAGGCGTGAGCCATTGCACCCAGCTGATGTTTTTCTTAAAATGCAAATTCTTTGGTTACACCCCATACCTACTGAATTTGTATCTCATGGGAAAGCTGTACAGTTTGTATTTTTAACTAGTATTGTTTATTTCTTGCTACTCAGAGTGGTCCCAAATTAGCATCTACATCACTGGAAACATTTTAGAAAAATAGAACTCCAGGCCCTGCTCCAGACCTAATGAATCAGAATAATATAGACATTCAAGTTAGAAAAGTACTAGGTAATCTTAATGTACACTTGGAAGTTTAAGAATAACTGATCTGGCCCCAACCTGTCATTTTAAGTTTGTCCCTCAATGTTGCTCTACATTTATTCATTCAACCAACATGTATTGGGTAAGGTATCAAGGATGTCTTCACATAGTCATGGAACTCTTAGTACAAAGTTGACAGAATATAATGTCTGCCCTCCAGAGACACACTGGGGTTAACCAGTGAAGTTGCTTACTGCTGCGGGTGACCAGCCAGTGGCTCTCACCGTCCATTTAGACTAAAGGGATCAGTATTTTGGGCACACCCATAACCATTCATAGTACCTTAGTTGGGGAGCTCTGCCTTATGTCCTGGTATTTCTTAAGATTCCTTTCTTGGCTCTCTTCCCACTGCACATGCTTCTTTGACAATCTCATTTACTTCCATGGCTCAGTCACATCTGATATCCACGTCCAATCAATCATGCAGCCCAGGTAATTTACCTCCTCAAAAGCTTTTAATTTGTCATTTGTCTTCATGTTTCTACCTTAGTTTAAGTTACCATCATTTCTTACAAGGAATATGCAAACTTCTGAACAGGGTTTACAAGGACCAGCATGATCTGTCCCGATATTACATCTTGACTCTCTGTAGCCCTAACATAATCTAGTCATCAACTCCTGAATAAGACATGGCTGTCAGTACTTGGCCTCTCCACACCAAATCATTGACTCAAGATTGTTTATTAAAGAAGGACCTGTGATGCTGTTGTCATTGTCCTTAACCTGTAAACTTGCTGCCTTCCTCACTTTCCATTTATTCTTTAACCCTCTGTAGTATTGCATTTGACTTATTACCCTGAATTTGTTGTTACAAAGGTCACTAAGAGTAACCAATTTCCATATTGCTGAATCCCATCCTTCCTTCTCTTCCTGGACCTCTTGATCAATTGATAACCTTTCATAACTCACTTTTCCTCTAAACTCTCTATTGCCTTCAGTTTTGCCCAATCTGAAGTGCCCAACTGTCCTATCCTGCTTCTGTAATATTTTCCCCCTTTTACCATGTAAAAAATAATTTCCTGATGTTCCCTTTGGGTTGCTCCAGAGACTTTTTCAAAGATTGGAGTTCTCCCAAGTTTTGTCTAAAGGTCACTGTTCTTATTCTCTGTTTTCAACTTGTCCGCTTCCAATCTGTTCTCCCCAGTGCAATAGGAGTGTCAGTCTAATTATGTCAAGCCTTCAGTGGTTTTTTAAATCTTTTCAGATGGAGTTGAGGCCCTATGTGGTCTCACCTCTTCTTTATCTCACCAGCCTTATGATCAAATTCTGCACTCCCAGACATAATAGCAATTAGAATAAGAATGTTTTCAATTGCAAGAAGCAAACAGAAAAACCCAACTCAAAATTATTAAATAATACAAAACAAAAAGTCAGGAGTTTGGAGGCTTCTGGGTTGGTTAACTCAGGAGCTCACTGGTATCACTGATGAACTAGGTTTCTCCATCCTTATGCTTTCACTTTCCTTGGGATATTGGTTTGGTCTTCCAGGATGGCTATTGCTAAAGGTAGCTGCAGTAATTTATTCTGTGTTTCTGTTTATCAATAAGGAGACCTTTCCCAGAATCCCTGAGCAGACACCTCATGCATGGCCCAATTGGCTAGATTAGTTATATACCCCTTCTTAAACCATATTGTTTGCCAATATGGCCAACAATGTGGGGTTGGTGATCCCAACAATGTGGGATGTGGGATTACCACAAATGACTTAGTCATGTGCTGGAGAAACAAAATTAGGGCTTCACAGCAAGGAAGAAGGGAGGAATGAAGTATCCTACTGTTATGTATACTTGTCTTTCTTCCTGTACATACACTAAAAAATGTTCAGGCCCATATGAAAAATGTATTTATTTCCCAAAGAGAATCAGCCAGAATCTCATCCAAATACTCTATCCAG
Seq C2 exon
CTTCATATCTAAGATCTCTGGTGGACTTTTTCTGCCCGTGGACGCCGCTGAAGAAGCATCGTTAAAGTCTCTCTTCACCTTGCCGTCATGTCTAAGTCAGCGTCTCCAAAAGAGCCCGAACAGCTGAGGAAGCTCTTCATTGGAGGGTTGAGCTTTGAAACAACTGATGAGAGCCTGAGGAGCCATTTTGAGCAATGGGGAACGCTCACAGACTGTGTGGTAATGAGAGATCCAAACACCAAGCGCTCCAGGGGCTTTGGGTTTGTCACATATGCCACTGTGGAGGAGGTGGATGCAGCTATGAATACAACGCCACACAAGGTGGATGGAAGAGTTGTGGAACCAAAGAGAGCTGTCTCCAGAGAAGATTCTCAAAGACCAGGTGCCCACTTAACTGTGAAAAAGATATTTGTTGGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGAGATTATTTTGAACAGTATGGAAAAATTGAAGTAATTGAAATCATGACTGACCGAGGCAGTGGCAAGAAAAGGGGCTTTGCCTTTGTAACCTTTGACGACCATGACTCCGTGGATAAGATTGTCATTCAGAAATACCATACTGTGAAGGGCCACAACTGTGAAGTTAGAAAAGCCCTGCCAAAGCAAGAGATGGCTAGTGCTTCATCCAGCCAAAGAGGTCGAAGGGGTTCTGGAAACTTTGGTGGTGGTCGTGGAGATGGTTTCGGTGGGAATGACAACTTTGGTCGTGGAGGAAACTTCAGTGGTCGTGGTGGCTTTGGTGGCAGCTGTGGTGGTGGTGGATATGGTGGCAGTGGGGATGGCTATAATGGATTTGGTAATGATGGAAGCAATTTTGGAGGTGGTGGAAGCTACAATGATTTTGGCAATTACAACAATCAGTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGGAGGCAGAAGCTCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAACCACAAAACCAAGGTGGCTATGGCGTTTCCAGCAGCAGCAGTAGCTATGGCAGTGGCAGAAGATTTTAATTAGGAAACAAAGCTTAGCAGGAGAGGAGAGCCAGAGAAGTGACAGGGAAGCTACAGGTTACAACAGATTTGTGAACTCAGCCAAGCACAGTGGTGGCAGGGCCTAGCTGCTACAAAGAAGACATGTTTTAGACAAATACTCATGTGTATGGGCAAAAAACTCGAGGACTGTATTTGTGACTAATTGTATAACAGGTTATTTTAGTTTCTGTTCTGTGGAAAGTGTAAAGCATTCCAACAAAGTGTTTTAATGTAGATTTTTTTTTTTGCACCCATGCTGTTGATTGCTAAATGTAATAGTCTGATTGTGACGCTGAATAAATGTCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139675-HNRNPA1L2:NM_001011725:5
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=21.8),PF0007617=RRM_1=WD(100=21.8),PF072928=NID=WD(100=14.0),PF116273=HnRNPA1=WD(100=11.2)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
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]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)