DreINT0046824 @ danRer10
Intron Retention
Gene
ENSDARG00000088593 | chst1
Description
carbohydrate (keratan sulfate Gal-6) sulfotransferase 1 [Source:ZFIN;Acc:ZDB-GENE-040801-21]
Coordinates
chr25:13921209-13924711:+
Coord C1 exon
chr25:13921209-13921735
Coord A exon
chr25:13921736-13922469
Coord C2 exon
chr25:13922470-13924711
Length
734 bp
Sequences
Splice sites
5' ss Seq
GAGGCAAGT
5' ss Score
3.32
3' ss Seq
TGAGATCTTTTGTTTTTCAGCTT
3' ss Score
8.02
Exon sequences
Seq C1 exon
AGCATTGAACACAGACGTGTTCAAAGGGAGGACGCGTATAGTGAACCAAATCTGCCTCCCCCCGTGCTGTTTTCCCCTCCCTCAGCCTTTGTCAACTGTGGTTTTGAGGGAAGGGGATGAATATTCGTAGGACTGTCTACGTTTGACTTAATCTGGGACCAACTGGCACACCTCTCTTCAGTCTTCTCCTCACGACAAACCAACGAAATATCTGTCCGGCGTTTCGCGTTTAGTCACAGAGAGATGTCTGAGGATGCGCATCAATACCTTATTCATCCGTTGTCTCTCCGCGGAGCCTGTCTTTGAATGTTTTCCCCGAGCATGAATGGGGCTGCTTGAGGATATACGACCTTTTCTTCGTTTTTTTAGGGAATAAGGAGCCCTTCGACATTTGGAGATATGAATTAAAGCGATAAAGCGTCTATGACGGGCGTTACGGGACGACTACGCGAAGCCATCACGGCATATGGTGATTTTTTTCTCTTTTGTTTAATTTTTCGTCATGTTCTCATACAGCTTTATATGAG
Seq A exon
GCAAGTATATCGAAGTGTTTATTTTGACGATATTTTCGAGGCAACTGGATTTCGGAAATGTTTCTGCTGGAATAGGGGGAATAAGTTGCTCACTGATTTATACAGTCAGATCGGATCTGCTATTTTTTTATTTTCAACTGAATACCGAGTTGTGTTGCACTGCGGTAAATCAGAACTCGACGCGCGCGGTCGACGACGGCTGCCTTTCAAACATTTCACAATAAGCATGCATATGGTATTGTGAGGGATTGCAATTAAAGCATCTCTCTACAGGTGCCTGAACTGGTGCCAGTTTGTGGAAAAGAAGCGATTTTGAAACCTGCCTGAATTCTAGACGCAGGTTTGCACGAACCTTTGCTGATTTCCCCAAGGGAAAAACAAAATACCTCAGGCTTGTGTAAAAGCCTGTAGGAAGCAGTTTAGTTGTAAGAGTTTGGCTGCATTAAAACGTTAAGTAGTTTATCAAAGTGTCATACTGCAATAAGCGACTGCTTAAGGCTTGCATTGTGAAGCAGAATGTAATGTAATATGTGTTGAAAGGAGATTTGCTTTTCCCAGAATTTAACAAGGAGTCATTCTAGTTTAAATCTTTAAATCCTAAATTTAAAATATGCTTTTTTGTTTCTGGTATTGACTCATTATTATAGCATGTTATATAATGTTATATACAATGCAAATTCATGTTCTGCTTTTTCCTGGTTTTCAAACTCACGCTGAGATCTTTTGTTTTTCAG
Seq C2 exon
CTTTGTCTTTGTGGATAGGATCAAATCAGACTGCATCCTCTAAATGAAGTTACCCAGCCATGCAATGTTCCTGGAAGGCTGTGATTCTGCTTGCATTGGTGTCCATAGCGATCCAATACACAGCAATCAGGACTTTCACAGCCAAGCCTTTTCATATTTGCCCTGTTCCTAACCCCCTGAACTGTGGTTTGGGGCAGGATGTGGAGTCGTTCGATCGGATGTGTGATGAGTACCCATATTTTAATTACAATTCCTCAAGGAAGACTCACATCCTCATCTTGGCAACCACTCGCAGCGGCTCCTCTTTCGTTGGACAGTTGTTCAACCAGCACTCAGATGTGTTCTATCTCTTTGAACCACTCTATCATGTCCAAACGACCTTAATCCCTCACCTTTCTCCCAGCAGATACGCTGTGGAGCGCCGAGTGATGCTGGGAGCCAGTCGTGACCTTCTTAGAAGCCTGTACAACTGCGACTTGTATTTCCTAGAGAGTTACATCAAACCGCAGCCGGCAAACCACACCACGGATAAACTGTTTCGACGTGGAGCCAGCAAAGCCCTCTGTTCTATGCCGGTTTGTGATGCTTTCAGCCCCAATGATGGCAATATAGAAGAGGGGGATTGTGTTCGGAAGTGTGCCTCTCTTAATTTGACCCTAGCTACCGAATCATGCCGAGAAAGACGGCATGTGGCCATTAAAACGGTGCGTATCCCGGAGGTCAACGATCTTAAGGCACTGATTGAAGACCCTCGGCTTAATTTGAAGGTTATACAGTTGGTAAGGGACCCACGTGGAATATTATCATCGAGGATTGAAACCTTCCGGGACACTTACCGCCTATGGCGGATCTGGAGAGCCACAGGCCGTAAACCCTACAACCTGGATTTGACCCAGCTCACGACAGTGTGTGACGACTTTCTGAACTCGGTGTCCACAGGTTTAAGCCGGCCACCGTGGCTTCGAGGACGGTACATGCTGGTGAGATACGAGGACCTAGCCAGAAATCCACTCCAAAAAACCAAGGAGGTTTATGAATTCCTTGGACTTTCGCTGGAAAAAAGTGTGGTGGACTGGATACATAACAACACAAGAGGCAATAACGATGTGTCAGCAAAGCATAAGTACGGCACATTGAGGGACTCGGCGGCTAACGCAGAGAGCTGGAGGTTGAAATTGTCTCATGACATAGTTGATTACACACAAACTGTTTGTCAGCACATTTTAGATGAGCTCGGCTACAAAGCTGTCAACTCCCCTGAGGAGCTGAAAAACATGTCCATCTCTCTCATTGAGGACAAAACCTTCATACCTTTTTTGTAACAAAGGTAATCACGTGCACGCACAACTATTTTTCTACATTTATATTCTTGCCTTAATGTGACTGACATTTGCACTATGAACCTTTTTGTAACTTCGGAGACTCCCTCGCAGTCCCCCCTCTATGATATTTCTGAACAGCACAAGAACCAAAACACTTAGCTGTAAAGAGATCTCAACTTCACCTTGATTGCGGCGATTGCATTGAGATAGGCAACGTTCCTTATTTATATATTAGAGCAGAGCACCACACTATTGACAAAGAAATTCTGTATGCTGGTCATTGCTTTGACAACAGTGAATGTGAAAATTTTGTCAGTCAAAGAACCCAGACTATTCTCAAGATAAACACTCTTCAATGTGGGACTGAAAAATGCTGTCATGTATAATTACAGCCGTGCAATAAAATTGTGAATGTCACAGTCAGACTATTTCTCAGGTTGTTTCTCAGTGCAAAGACTTGACTGTCAGAGAGCTTTCTGGGGGTTTATGCTCGTGTTTGATTTGCTTTTAGAATGCATAATGTGCTGGAGCTGTACCTGGGTTAAAAAAAAAAGAAAGAAAGTAAACTCACAGTAAAAGCACTTCAGTGTGCTTGCATTGTTTGGTTTACAAATTAGTTGTAAAAACTCAATGACCACTGTTTCGCCACAATGAAGGTTTCTGTTATATTTTTGCCAAACGCCATGACACTATTTCAGAGAAATCCAATGCAATCAAGTTTTTAAAGTCGACAGTTTGTTAGTTTAGAGGTTTTCATATGAAATGCATGGAATTATTCATCCTTTAGAGGCTGCCCTCATCATCATATAACAATTTTTCATTGATTCAGTGCATAGGGATTTGTATTCAGTGTTCATGGGAAATCGTTCGACTCAATGTATGTGAAAGAGGCTATTTTTTAATAAATGTAGAAAAGCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000088593:ENSDART00000125733:1
Average complexity
IR
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=79.8)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGCCCTTCGACATTTGGAG
R:
CAAACCACAGTTCAGGGGGTT
Band lengths:
342-1076
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]