RnoINT0036366 @ rn6
Intron Retention
Gene
ENSRNOG00000007989 | Chst1
Description
carbohydrate sulfotransferase 1 [Source:RGD Symbol;Acc:1308142]
Coordinates
chr3:81509385-81512807:+
Coord C1 exon
chr3:81509385-81509514
Coord A exon
chr3:81509515-81510703
Coord C2 exon
chr3:81510704-81512807
Length
1189 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TGGCTGTCTTCTGCCCACAGACC
3' ss Score
11.41
Exon sequences
Seq C1 exon
GTAACTGCTGTGTGTGCTGCATGTGGTTGGAAGAAGACCCCTGTCCCCAGCTGTTCCTTTGGAGCGACCTTCTCTACCTGAAGGCCTGGGGTGAGCCACCTCCATCCCAGGACCAGCTGAGTTCCAGAAG
Seq A exon
GTGAGAATTGTTTCCATCCATTTCTAATTCAGAACCCACCTAGGCTGGTGGCCTGAGACACTTGGGCACACAGGCTAGCCAGCTCCTGCCCACAGGAGCCCTAGTGTGGGGAGAGGGATCATGGCTTGTTAGGGGTGGGACATAGAGGTTGCAGTTTGACAGTTGGGGCTGCACGGCTTAGGGGTGATGTTAGATCGGCTGGAGCCCTGAGATAGCAGTCAGTGTGAGGAGCAGGAAAAGTCATGTTTTGTGGCCTGAGGCAGAGCGCAAATCACTGGTCCCCTTTACAGCAGTCCTTTGGTAAGTGTTGAGCTCCTTGGCACTGAGTCTGGAAGCATCCCTGGCATCTCTGGTGGCTGAGGCAGCATGCCTTGGGGTATATTGTGAGCCCGTGGCATAGGCTTCCCTTTCCCATTTTCCCATACCCTTCCTCCCCCTCCCCCACTTTTATGGACCAGAAACAAGCTGAGTCCTGTGCAGAGAGACTTAGCCTCTGGAACCTGCCCTTGCTCCAGGCCAGTTGACTCACAACACTGCAGGTGCCTGGAAGTCCACATCTGGAGGTAGCTGGGCTTCCTCATTTGCAAGGTAGAAAGGCCATGGCCCAGGGTGGGCAGTTCCTGGTCCAGCTGGGTTCTGTTGTCAACTCAGAATTCATGGGGCACAGGGCTCCCTGCTCTCCTGGATTTGTTTGTGGAGGGGAATTTGGTGTGTATCCTTCCTCTAGGGGTAAAAAGAGGACATAGAAAAAGACCATGGTCTGGGAGGGTGAGTATCAGCCTGTGTGATTAGAAGATGCTTAAAATCCAGGAAATGCAGGCAGGGATCAAAGGAGTGTTGGGGTGTGGCATGAGTCATTCCCTGAGCCCCCTCCCCTAAGTGTGGAAGTTGGGGGAGTTGGGCTTTGACATAGTAAGTAGACTGGGCTAGGAAAACCAGAGCTCAACATAGGAGGCCTCTGCAACCACAATTCATTTAGCTCTTGGGGTTCATGGAGTCTGTCTAGCTCTTTGAAGCTCCCAGGAGACACCAAGAAGATGACAGTTGAGTGTGTGCTCTGTAGGTCCTACAGGATGTGTGATGGGTAGGGGCTGTGTGAGCACCGGGTTGGGGCTGGGTATTTTCCTGGATCCCATGGTGGCTCTTGGCTGTGGGAAGCACTTAACCCCTGGCTGTCTTCTGCCCACAG
Seq C2 exon
ACCCCGTGCCTTGGAGCAGCAGCCCCATGACGGTGCCCAGCCATGCAATGTTCCTGGAAGGCTGTCCTCCTCCTCGCCCTGGCCTCCATTGCCATCCAGTACACAGCCATCCGCACATTCACTGCCAAGTCTTTCCACACTTGCCCTGGGCTGACAGAAACTGGGCTGGCAGAGCGGCTGTGTGAGGAGGGCCCCACCTTCTCCTATAACCTCTCCAGAAAGACCCACGTCCTCATCTTGGCCACCACACGCAGTGGTTCATCCTTTGTGGGCCAGCTCTTCAACCAGCACATGGATGTCTTCTACCTGTTTGAGCCTCTCTACCACGTCCAGAACACGCTCATCCCCCGCTTCACCCAGGGCAAGAGCCCCGCCGACCGCAGGGTCATGCTAGGTGCCAGCCGGGACCTGCTGAGGAGCCTTTATGATTGTGATCTCTACTTTCTGGAGAATTACATCAAGCCACCTCCGGTCAACCACACCACCGACCGGGTCTTCCGCCGAGGGGCCAGCAGGGTCCTCTGTTCCCGTCCTGTGTGTGACCCTCCTGGGGCCTCTGACCTGATCCTGGAGGAGGGGGACTGTGTGCGTAAGTGCGGCTTGCTGAACCTGACCTTGGCAGCTGAGGCTTGTCGTGAGCGCAGCCATGTGGCCATCAAGACTGTGCGGGTGCCTGAGGTGAATGACTTGCGGGCCCTAGTGGAAGACCCCAGGTTGAATCTCAAGGTCATCCAGCTGGTGCGAGACCCTCGTGGTATCTTAGCTTCTCGGAGTGAGACTTTCCGGGACACATACCGACTCTGGCGGCTTTGGTACGGCACAGGGAGGAAGCCCTACAACCTGGACGTGACCCAGCTGACCACAGTGTGTGAGGATTTCTCTAGCTCTGTGTCTACTGGCCTCATGCGGCCCTCCTGGCTCAAGGGCAAGTACATGTTGGTACGTTATGAGGACCTGGCCAGGAATCCAATGAAGAAGACAGAGGAGATCTACGAATTCCTGGGTATCCCCCTGGACAGTCACGTGGCACGCTGGATCCAGAACAATACGAGGGGTGACCCCACTTTGGGCAAGCACAAATACGGCACAGTGCGCAACTCTGCAGCCACAGCTGAGAAGTGGCGCTTCCGCCTCTCCTATGACATCGTGGCCTTTGCTCAGAACGCCTGCCAGCATGTGCTGGCACAGCTGGGCTACAAGATGGCCACCTCGGAGGAGGAGCTGAAGAACCCAGCCATCAGCCTAGTGGAGGAGCGCGACTTCCGCCCTTTTTTGTGACCTGGGTGTGGTGGGGGTGGGAGGCAGGTGGCTCTGGTTTTGCTGATGTGGACCTACTACGGGCCGTTTTTTAACTGTTGCCTTATCTCTCTCCTCCCTCTCCCACCCTGTTTGTGTGTCCTTTCCACACAATCCCCCACCCCGGGTCTACTCCTCTCCCACGCCATCTGCGCATCCTTCTTGCCCTTGTCCACTCCCTTTCCTCCTGCCTCTTTCTGCCCCTGAAATTTGCACTATGTCTCTGGAGGGGAACACTGGGCAGAGGGCGTGTGATGGGGGTTACAGCCCCCCACCCCATTTAGACACAAGGCTGCTGGGTCTCTATGCGGATGGGGACAATGTTTACAGGCACCCAGTCACACATTCACGTGTGCACACAGGCACACGACGAGAGGCACCCCAGCACATAGCTTGTAGTTTTTGCAATTGTCTTCTCCAGGTAATAGGATGGACACAAAGGGGCCACACCCCCCAGTTTAAGAAAAGAGTCCATCCCAACCCCCTCCCTGCTCCTCCCCTGGAGCAGGGCACCCATCCCTCCTGCACACCCTTGCCTGGTGGTGAGCAGGGTTTTACTGTGAGGTGAATTGGGATTACTTTCTTTCTATTTGGTTTGTGGTGAGCTTGTCTGTCTGAGTCTTGTGTCTACCCCTAGACCAGTAATGGCTAATGAATCTTAGAAATTTCTGATTGATCTTGGGGTCCCTCTGTGATATTTCTTTGTGCCAAAAAGATATAAAAAAAGACAAAAATATGTGAATCAGTTTGCTAAATGAAAATTGAAATGCTTTATTTGTGTTTTCTGTAAATAAAAATGTGCAGCACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007989:ENSRNOT00000010510:2
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=78.9)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
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:
TGGAGCGACCTTCTCTACCTG
R:
TTGAAGAGCTGGCCCACAAAG
Band lengths:
355-1544
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]