HsaINT0116405 @ hg19
Intron Retention
Gene
ENSG00000142233 | NTN5
Description
netrin 5 [Source:HGNC Symbol;Acc:25208]
Coordinates
chr19:49164664-49166800:-
Coord C1 exon
chr19:49166720-49166800
Coord A exon
chr19:49165299-49166719
Coord C2 exon
chr19:49164664-49165298
Length
1421 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
GACATCTCCCCTCCCCACAGTTC
3' ss Score
10.59
Exon sequences
Seq C1 exon
ACCCTCAGTGTCAAAACTACTGCAATATGTCGGACACCAGGGTACACATGAGCCTTCGGAGGTACTGCCAGCAGGACCATG
Seq A exon
GTGAGTGCTGGGGAGACAGACAGCTGAAGGCTACACAGCTGGTTCTGATGACTGCTTCTAAGCCACCCCCTTTCTGGCCTTCCACTTTCTCATCTTAAATGGGAAGGAGTGTTGGATTCCAAACCCCTTCCTGATCTAGAAATTGATGGGGCAGAAGACAAATGGGGAGGGGAGTGGGGAGGGGGCATTCACTACCTTCCTGTGTCTCCTCTTTCCCCATGTTCTTCGGCTTACAGAGTTTCATCATCTCCTTCAGCCTGACATCTCTGAGGGATGGAAGAGATAGGGGAACTGGTTGAGTGGAATGAACTCTTGCCCTGTCCTCCCTATCTCAGAGACCCTTTCTGCTTCCCTTCATGGTCCCAGATATTTGAGCCTTAGCCCCACTTCCCATAAAGACTTGTCCCACGGTTCCCTAATCCCCAGTCCACACCTGCTCCATGACCTTGGGGTCTATGACCTCAGGCTATTCAGCTCTCTTAAGACACTCAGGAGTTCGGCCCAGCCAACAAATCTAGACCAACGCCAGCTATTTCTCTCAATGTATAGGACCGCAGACTTCTCCCTCAGGAACCTCATCTGGTCACTAGTGTTCTAGGCCTTCACAGGTGGAAAGATTTTCCCCACCTTCCACAGGGATCTCCTGCCCCGCAGACCCAGCTGGCTAGTCAGAGTCCCACCCAGCCTCTCAGAAAGTGCATTTTTCTGGCCGGGCGCGGTGGCTCATGCTAATAATCCCAGCACTTTGTGGGGGCCGAGGTGGGCGGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAAAAATTAGCCAGGCGTGGTGGCAGGATCCTGTAAACCCAGCTGAGGCACAAGAATCACTTCAACCTGGGAGGCAGAGGCTGCAGTGAGTTGAGATCACACCACTGCACTCCAGACTGGGCAATAGAGTAAGATTCCGTCTCAAAAAAAAAATTTATGTTTTTCTGAATCACTATCAGTATGACCTCAGCCCTCACATTCCAGGGACCAGTCTCTTCCTTCTTCTGGTCCTCGAAATTTATCCCAGAGCCCCTCCCCCGGCAATGTGACCCCTCCTTCCCAAGAATTCCACCATTGATACCTTCTGACTCCACTGCATTAGAGACCCTGGACCTGCCTCTTCTGCCCTGTCCCCAGCCCCACCTACTATAGTTTAACTCCTTATCTCAAAGATGTTTCCTCCAGCAGGCTCTACCCCTCACGATTTAGGGTCAAACTCTCCAAGGTTCAAGGTTTCTCTCCCCACTGCGATACCAGAAGCCCACCCACCGGTCTCGGGCTCCTGCCCACTGTGACTGACCCCACGGGACCCAGAGGTACCCTGGAAGCTCCCCACGACCTGGGCTGACATCTCCCCTCCCCACAG
Seq C2 exon
TTCTCCGCGCGCAGGTGCTAGCGTCCGAGGCGGCGGGCCCGGCATGGCAGCGGCTGGCCGTGCGCGTGCTGGCCGTTTACAAGCAGCGGGCGCAGCCCGTGCGACGCGGCGACCAGGACGCCTGGGTGCCCCGCGCCGACCTGACCTGCGGCTGCCTGCGCCTGCAGCCAGGCACCGACTACCTGCTGCTGGGCAGCGCCGTGGGCGACCCCGACCCCACGCGCCTCATCCTCGACCGCCACGGCCTCGCGCTGCCATGGAGGCCGCGCTGGGCCCGGCCCCTGAAGCGGCTGCAGCAGGAGGAGCGCGCCGGAGGCTGCCGCGGCGTGCGGGCACCCACACCCAGTCCCAGGCCGGAGCACTAGACGTGAGATGGGGCTGCCTCGAGCACCAACAAAGTAATTTGGGAGCGACTAGGAGCTGAGCCTTCTACCTCGACGGTGCACTGCAGAGAGCCAATCAGACGTCGCAGAGCCCCGACGACACTATGCTTGCGCCCACGCCGAGCAGGCGTGCGGAACTTTTAGCAAAAGGCGGCAAGCGGGACTTCTGGTCCCAACATTTCCTCCTTTGGCCTGTGGCTTATTCCCCGCCAGTGATCTGTTTCCCCCAATAAAGTCTCAAATCTTTGGGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000142233-NTN5:NM_145807:6
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.240
Domain overlap (PFAM):
C1:
PF0175916=NTR=PU(23.5=28.6)
A:
NA
C2:
PF0175916=NTR=PD(91.7=81.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAGGGTACACATGAGCCTT
R:
CTGCTGCAGCCGCTTCAG
Band lengths:
345-1766
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)