HsaINT0154494 @ hg19
Intron Retention
Gene
ENSG00000187122 | SLIT1
Description
slit homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:11085]
Coordinates
chr10:98757795-98762126:-
Coord C1 exon
chr10:98761915-98762126
Coord A exon
chr10:98761108-98761914
Coord C2 exon
chr10:98757795-98761107
Length
807 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGG
5' ss Score
6.23
3' ss Seq
TTGGTGTCTGTCCCATCCAGAGT
3' ss Score
7.13
Exon sequences
Seq C1 exon
GTGTGTCCATGGGCAATGCGTGCCCCTCGACGCTCTTTCCTACAGCTGCCAGTGCCAGGATGGGTACTCGGGGGCACTGTGCAACCAGGCCGGGGCCCTGGCAGAGCCCTGCAGAGGCCTGCAGTGCCTGCATGGCCACTGCCAGGCCTCAGGCACCAAGGGGGCACACTGTGTGTGTGACCCCGGCTTTTCGGGCGAGCTGTGTGAGCAAG
Seq A exon
GTCAGGGGCCCCCCTCCTGACGTGCCCTCCCCAGGGTCCCCCACAAATTGCTTTAGCAATTTGACTCTTCCTCCCAGTCTCGGCAGCCCTTCTGTCCCTTCCCAGCCCTGTACCATGGGCTACTATGGGGCTTTCAGAGTCCCTCCACCCTCTGGGCACTGCTCCCAATCTCTCCTGGCCCAGTTTGCCCTGCAGCTCCCTTATTCAGGGTATGCGCCTCTTCTGGCTGGGGTCTCTCCTTGCAGAAGAGACCACCCAGGGTAACAGCTCCTGGCCCAACCTCTGCCTCTTGGCCCCATCACCTCATGACCTGGGAGCGGCAGCAGGAAGTCCGAGGGTTGGGGACTCCTTCCCAGGCCCTCCCTGGCCTGCTTGACCAAGATGGCTTCTGCTGGAATCCGGACTGCTAAGGCTGGGCAGGGAGAAGCTGGAGAAACCCAGAACTCAGGCACCTTAAGGGTCCCCTAGGCTATCCCCTCCCCAGCATGAATCCTTTTCATAATGTTATTGCCCCCGGGGCCTCCAGCCTCTCTTGCACGCCTCTAGCAATGGGGACCCCCCCTCCCTCCAGCAGTTCAGTCTGTCCTGGAGGGCCCTGACGCTAGGACCAGACTGTAGGCCCTGGGAGGAAGCTTGTGCATGTCAGTGGGAGGCGGAAGTATGCTGGGGACAGAGGTGGGGTCTGAGAGCCAAAGGATCCACCCCACAGATGCTGCCCTCCTCCTCCTCTTCCTCCTGCCTCCCTGGAGGCAGCAGCTCACCCATGGGTGTGCCCTGAGGCTTTCTCTTGGTGTCTGTCCCATCCAG
Seq C2 exon
AGTCCGAGTGCCGGGGGGACCCTGTCCGGGACTTTCACCAGGTCCAGAGGGGCTATGCCATCTGCCAGACCACGCGCCCCCTGTCATGGGTGGAGTGCCGGGGCTCGTGCCCAGGCCAGGGCTGCTGCCAGGGCCTTCGGCTGAAGCGGAGGAAGTTCACCTTTGAGTGCAGCGATGGGACCTCTTTTGCCGAGGAGGTGGAAAAGCCCACCAAGTGTGGCTGTGCCCTCTGCGCATAGCGCTGGGCGTGGACAGGCCGGTGAGGGCGGGCAAGGGGCCCCAGCCGCTGCAGCAGCGGAGACAGTCGCCAGCAGCTGGGCTGGGGTGCAGGTCATCACAGGACGGCTCCTGGGCAGCTGGGCCCTCCTGGGTGGGGTGGTGCCAGAGCAGCCTTTTAAAAGCAAATTGCGCCATAGCTGGGGGCAGCGGGGGTGGGCGAGGCCTGAGCTGCGGGCTGCCCTCTCCGGAAGTGCCTTGCACAAATAGGCGCTTAATAAATATTTGTTGAGTGAATGTGTGCGTGAGGTCAGGCCAAGAAGTGCAGAACGATGACACCCCTCCTTACCTGCTATCTGAATCTGGAGAAGAAAAATGACAGCCTTCCAAACCAACCCTTCCCTTTGGCCTGTGGCCCAGGCTGGCTTGGAACTGGGTCTGTGGCCCCAGAAGCCTCTTACCCCTCTGCGGGCAACCATGAAGTACTGTCAGCCTCCCCGGGAAGCCAGCCTGGTTCATTCTGCTGCTACAGAATCTGCTGGTGGTAGGCCAGGCTCTGGAGCGGGGGTGCCGCCTCCTGCTGGCCAGGGAGGGTCGGACCCTTGCCCCCTGGGCTGACTGGCAGCTCTGCAGCCACGGCTTGGGAACGAGGCTGTGGGTGGAGGTGGTTCTTAGGACCAGGCCTCTGAATCCTAAAGTTCTAGCATGACTACTGTAGCTGCGAGGGCTTATGTGGAGGAAACAGTCACAGGGGCTGCTCAGGGTGGCAGACCCCACTAAAGAGGGCAGAGGGTTCTTTGCTCTAGATAAACAAACATCATCTGCCTCCAGACACTGGCCACAGTAGGAGTATTGGTCCTGGGCTTCCCCAGCCACCAGTCAGCCACAAGCTGTCGGTGACCTATTGGTAGAGGGACTGGGTGTGAGGGTCTGGGCCAGGGTGCTTGACCTGGGAGCAGCTGGTTCAGAGTCCTTCACACCGCAGGCCAGTAGGGAGCAGTGGAAGGGACAGTGCTCCAGGCATTGGGAAGTCCCTGCTGGCTCTATCACTCGGGGCAAACTTCTCCCCACCTGGGCCTTGGGTTCTTCAGCTATAAAATGGCCAGAGGTGGGGGGCGGGATGACTAAAGGAACAGTGCAGACTCCCCCACTGTGGTCTTGGGAGGCCAGAGGAGTTAGAAGACCTATCTATCTATCTATCTATCTACATTGATCACATCAAAAGTATTTATGTGCCTAACCCGGGGCTGGGGATTGTGGACGTTCTGGCCTAATGGACAGATGTGAACTCATCCCAGAGCATCGCAGGAATGACCAGGATGCCCGGGAAGAGTTGAGCTGAGTGGGGGCTCCAGCCACAGACAGCGGCCCAGGCCAGGGAGTTGCTGGCAACGAAGGAGCCAGTGGTGGAAGAAGAAGAGGCCCTGAATATACGATTGCCTGCCCACGTTGTCTTCTCTTCCATACACAGTGAAAATGTAGAAAGATGGTTTGTGAGGCCAAACTGTGAATGGGCTAAAGGGAGGCAAAGTTGCACTCTCCTTCCCCAGAGGGCTCACCAAGAGGGCACACCCCCGGGGGTTCTGGTGGGCAACGGGGGTGAGCATGTCCCTGCCCTGGCTCCCTCCATCTGTGACCAGGAGGCATGGCTGGGTGTATGTTCAGGTGAGGCTCAGAGTGGCATTGTGTCCCTGTCCCCTGCCCAGGGCAGTGAGGGGAGCCCTTGATGCTGATTAGAAGGCTAGAACTGGGGTAGAGGTGCCTGGCATGTCTCATGCCATGGGGACTCAATCTAGCAACTGTGAGTCCTGGGGTCCCTGTGATGGGAAGAGGGCAGTGCCCTGCCCAATGTGGCAGGTGTCCTCATGGCAGGATCTGCCCCTCACCAGGGGGCTGGGATCTACTTGCTTGGAGCTCTGAGCAAGGCCACAATGCCCGCCCCCACCCCCAAGTAGACTGCAGCCTGGGCCTCATGGGGCTTCTCCCAGGCCCACATGGCATCCCTCTCTGAGTTTCCAGGCCACCGTGGGACCCTGCAGAGCATCTGCACCGGGCTGGATAGGGCAGAAAAGCTCAAGGGCAGCTAGCTTGCCTCTTCCCTGGAAGAAAGGTGCTCTGGGACTCACCAACCCTGAGAAAGATAGCTTTCCTGGCCACCACCATTCCCCACCACCCTGGAGAAGCCAATTCCCAGGCTTGAAGGGCACTGGCTGGCAGGAGGCCTCTTCATTCTGCAGGAGGTGGAAAGGACACCTGTAGACAGGTGATGCTCACCCCTCACCTGGCGCCATGGGGCTGGGAGGTGAGCGGCTGGCATGTTTGTTCCTAGGGAGCACCATGTGAGCTTAAGGCTCCCCTGACCGGCCCCACCACATGGCCCAGCCTCCTAGCACAGCAGCGCTGACCTCAGTGCAGTCTGAGGATTGGAATCCACCATGAGATGATGTGAGAGCTGTGTGCCCCAGGATCAACTTTTTCTCCAACTTGGCCATCAGCCAGCGAGTTGCTAAGGACCTGAGTCAGCACTCACGTTGCCTATTCACACTCCGCTTGAAAGTCCGGAAGGTGGCTACTGCAAAATCACCCCTCTGAGAAGTCCTCTCTCCACATCTTGTCCCCCTTTGTGAAGACCCCTAGTTCGCTCTGCATTTTAGGCATGAAGAGATACAGCAGGGTGCGTCCGGAGGGAGCTGTGGCCTTGCAACACCACTGGCAACAGGGCCGGGGCTCCCGGTGAAGGTGTCAGGAAGTGGAAAAGGCTGGACTTTGTCTCCTCTTTGCCTGCTGGTAGCCTAACCGCAAAAGTATCTCTTTATACAGAATACTTACAGATTCTAATATATATTTGTATTTCATTTTGTTACAGTATTTTTATATGTTAAAGTCAACATCCAGCGTCTTGTTTTGCCTTTCAGATGCTATGTGGTCGTGGCACGTTTTGTTGGGGGTTTCTGTAGTCGTCTTGTTTGGATCAACTCCTAGAGGCTGGTTTAGAACAGGCCCATGAGGGAGCTGCACCTGCCCTGGAAGTATTGTTTTAGACTATGTCGATATTGTCTGTTGTCTTCCATGTGAACATGACATTGAGTCACTCTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000187122-SLIT1:NM_003061:36
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.032
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(66.7=36.1),PF126612=hEGF=WD(100=18.1)
A:
NA
C2:
NO
Main Inclusion 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:
GCTCTTTCCTACAGCTGCCAG
R:
GGTGAACTTCCTCCGCTTCAG
Band lengths:
342-1149
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
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)