HsaINT0035272 @ hg19
Intron Retention
Gene
ENSG00000175264 | CHST1
Description
carbohydrate (keratan sulfate Gal-6) sulfotransferase 1 [Source:HGNC Symbol;Acc:1969]
Coordinates
chr11:45670427-45673640:-
Coord C1 exon
chr11:45673543-45673640
Coord A exon
chr11:45672516-45673542
Coord C2 exon
chr11:45670427-45672515
Length
1027 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
CTGGCCGCCTTTGCCCACAGACC
3' ss Score
10.82
Exon sequences
Seq C1 exon
TCTGCTGGCCACAGGGCTGCCGCACTGGCTGGGACTGCCAGCTGGGCCTGGAGACGCTGGTGGCTGTGGACTCCCCAGCTTGGAGCAGTCCCTCTTTG
Seq A exon
GTAAGTGGTTGAACCCTCCTGTGTTCTCCCCAGGAGCAGCCCCAGCCCCCACTCAGGTCTGGTAGCTGAGCCAGCCTCCAGAGAGGGTGCCTACAGGATGCTCAGGTGGGCTCCTGGCCCCGGACTCTCAGCGGCCCCATTCGCTCTTTCTGCTTCTCCATGGTCCCTCCCCAGTCCCCCTTCTGTGGGCAGAGGGGACACAGGAGGTAAGAGGGGAGGCCCCTGACTCCCTAAGATCTTCTTTGCAGGCCAGTTCACTCTGTGTCAGTGGGGATTATGTCACCTCCATGGCCTGGACCCTTGTCCCTAGAGACCAGGAACAGACCCTGGGTGCTGGGAAGGGTTGCCTCTCAGCAGACCCTGGACATCTGTCTCTGCTCCAGAGACTCTTAGAGACTCCACAAGCCCCAGAAGTCTACATCTGGAGTAAGTGGTCACCTGCATCCATGAGTTGGAAGGGGCTTGACACAGTTGTCCACCTTGCCTGGCCGTGCTGGCAGCTCACCGACCATGGTCTGCAGGGGTCCTTCATGCTCAGGGGATTGGGGTCAGATGGAGGCATCTGATAGGGACTCTTCTTTCCCCTAGGGATGGGCAGAGGACAGAGGAAAGAGGACCACCTGGAGAACTGGGCGCCAGCTCGTGGGGGTGGGAGACGCTGGCAGTGAGGAGGGGCAGTGTTTGAGGCAGGCCCTCGTCATTTCCTCAGTGTGGGAGTAGGGGGAGTCAGGCTCTTGCCCCGTGAGGCCCCTCTAAGGAACTCAGAGCTCAGGATAAGAGGCTTCCGCAGCTGTCCGCAGGTTAAATCCTGGGGTGCAAGGAATGTTTGTTCAGCTCCCCAAAGCTCCCAGGAGTCCCCCAGAGAACGGTAGTCTAGTGTAGAAGCTGCTTAGGTCTTCAGGGTGTGTGGTGAGCACTGGACAGGAGCCGGGCCTTTCCCTGGGCCCCTTGGAGACCGGCTCTTCCAAGGGACAAGCCAGTGCCCCCGCCGTGGAGGCACCTGACCGCTGGCCGCCTTTGCCCACAG
Seq C2 exon
ACCTCACCCCTTGGAGAAGCAGCCCCATGAAGGTGCCCAGCCATGCAATGTTCCTGGAAGGCCGTCCTCCTCCTTGCCCTGGCCTCCATTGCCATCCAGTACACGGCCATCCGCACCTTCACCGCCAAGTCCTTTCACACCTGCCCCGGGCTGGCAGAGGCCGGGCTGGCCGAGCGACTGTGCGAGGAGAGCCCCACCTTCGCCTACAACCTCTCCCGCAAGACCCACATCCTCATCCTGGCCACCACGCGCAGTGGCTCCTCCTTCGTGGGCCAGCTCTTCAACCAGCACCTGGACGTCTTCTACCTGTTTGAGCCCCTCTACCACGTCCAGAACACGCTCATCCCCCGCTTCACCCAGGGCAAGAGCCCGGCCGACCGGCGGGTCATGCTAGGCGCCAGCCGCGACCTCCTGCGGAGCCTCTACGACTGCGACCTCTACTTCCTGGAGAACTACATCAAGCCGCCGCCGGTCAACCACACCACCGACAGGATCTTCCGCCGCGGGGCCAGCCGGGTCCTCTGCTCCCGGCCTGTGTGCGACCCTCCGGGGCCAGCCGACCTGGTCCTGGAGGAGGGGGACTGTGTGCGCAAGTGCGGGCTACTCAACCTGACCGTGGCGGCCGAGGCGTGCCGCGAGCGCAGCCACGTGGCCATCAAGACGGTGCGCGTGCCCGAGGTGAACGACCTGCGCGCCCTGGTGGAAGACCCGCGATTAAACCTCAAGGTCATCCAGCTGGTCCGAGACCCCCGCGGCATTCTGGCTTCGCGCAGCGAGACCTTCCGCGACACGTACCGGCTCTGGCGGCTCTGGTACGGCACCGGGAGGAAACCCTACAACCTGGACGTGACGCAGCTGACCACGGTGTGCGAGGACTTCTCCAACTCCGTGTCCACCGGCCTCATGCGGCCCCCGTGGCTCAAGGGCAAGTACATGTTGGTGCGCTACGAGGACCTGGCTCGGAACCCTATGAAGAAGACCGAGGAGATCTACGGGTTCCTGGGCATCCCGCTGGACAGCCACGTGGCCCGCTGGATCCAGAACAACACGCGGGGCGACCCCACCCTGGGCAAGCACAAATACGGCACCGTGCGAAACTCGGCGGCCACGGCCGAGAAGTGGCGCTTCCGCCTCTCCTACGACATCGTGGCCTTTGCCCAGAACGCCTGCCAGCAGGTGCTGGCCCAGCTGGGCTACAAGATCGCCGCCTCGGAGGAGGAGCTGAAGAACCCCTCGGTCAGCCTGGTGGAGGAGCGGGACTTCCGCCCCTTCTCGTGACCCGGGCGGTGCGGGTGGGGGCGGGAGGCGCAAGGTGTCGGTTTTGATAAAATGGACCGTTTTTAACTGTTGCCTTATTAACCCCTCCCTCTCCCACCTCATCTTCGTGTCCTTCCTGCCCCCAGCTCACCCCACTCCCTTCTGCCCCTTTTTTGTCTCTGAAATTTGCACTACGTCTTGGACGGGAATCACTGGGGCAGAGGGCGCCTGAAGTAGGGTCCCGCCCCCCCCCCCCCCATTCAGACACATGGATGTTGGGTCTCTGTGCGGACGGTGACAATGTTTACAAGCACCACATTTACACATCCACACACGCACACGGGCACTCGCGAGGCGACTTCTCAAGCTTTTGAATGGGTGAGTGGTCGGGTATCTAGTTTTTGCACTGTCTTACTATTCAAGGTAAGAGGATACAAACAAGAGGACCACTTGTCTCTAATTTATGAATGGTGTCCATCCTTTCCCCATCCCTGCCTCCTGCCCCTGACGCCCATTTCCCCCCTTAGAGCAGCGAAACTGCCCCCTCCTGCCCGCCCTTGCCTGTCGGTGAGGCAGGTTTTTACTGTGAGGTGAACGTGGACCTGTTTCTGTTTCCAGTCTGTGGTGATGCTGTCTGTCTGTCTGAGTCTCGTGGCCGCCCCTGGACCAGTGATGACTGATGAATCTTATGAGCTTCTGATTGATCTCGGGGTCCATCTGTGATATTTCTTTGTGCCAAAAAGAAAAAAAAAGAGTGGATCAGTTTGCTAAATGAACATTGAAATTGAAATGCTTTATCTGTGTTTTCTGTAAATAAAAGAGTGCAATAATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000175264-CHST1:NM_003654:3
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:
PF0068522=Sulfotransfer_1=WD(100=78.9)
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:
GCTTGGAGCAGTCCCTCTTTG
R:
TGTTCTGGACGTGGTAGAGGG
Band lengths:
358-1385
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)