DreINT0050614 @ danRer10
Intron Retention
Gene
ENSDARG00000014670 | colgalt2
Description
collagen beta(1-O)galactosyltransferase 2 [Source:ZFIN;Acc:ZDB-GENE-070222-1]
Coordinates
chr8:19338788-19340677:-
Coord C1 exon
chr8:19340558-19340677
Coord A exon
chr8:19338862-19340557
Coord C2 exon
chr8:19338788-19338861
Length
1696 bp
Sequences
Splice sites
5' ss Seq
TGAGTGAGT
5' ss Score
6.51
3' ss Seq
TCAAATGTCTTTTCTTGCAGTCG
3' ss Score
8.91
Exon sequences
Seq C1 exon
GTGTACAGATGTATGTGTGTAACAGAGAACATTACGGGTTTCTGCCTGTCCCTCTGAAGGCCCAACAGAGTGTTGAAGATGAAGAGGAGAGTTTCACACACACCATCACTGAGGCCATGA
Seq A exon
GTGAGTATTAACACACGTTATACATATGAATATGTCTATTATAGAAATGCAAAATGACATACGCATGTGTATGATGTTTGCTTTGAGTTTTTCCAAATATATCCACACTTTGGAGAAATTGGATGACAGTCTTTCTAAAACATTTCAGGAGACGATGGGTGTATATATAAAACTTTGTGCTTCTGTTTTAATCAAGTGGTAAAAATACCGCATTCCTCAAACTAAATAAAGTGTTTAAGGATGAATATTAAAAGCAACATTATTCAAAATTAAGGCTGAAGTTAAGAAATTACAGAAATAATAGTTATTTTTGACATTATTGTGTACATCAAAAGCAGCTTGTTTCCGTGCATCTCCCATCCTCGCATATCATAACAGATGCTCAGTATTTAGTATTTAAATGTTCAATCTGATTGAGGTTTTACAGTACCAATCAATCTGGTGTGGGTTTTCCAAACAACAGCATAACTCATGGATTAAAAACCATAGTATGATTATAAACAGTGTACTTTAAAGTATTTCCTAAACTCTGTCAGAATGGAGCCAGATCAGTCTAAAACAAATACATTTACAAAATATAATGCATACATCCACAACACAATTTACATTAACAAAATACAATTCGTATTTATAAATACACTAATTCAATTTGTAAATTCACAATTCGATTCATAAATAGACTTATCCAATTCATAAATTCAAAACATGATTCATAAATACACAAATCCAATTAATAAATTCAAAACATGATTCATAAATACACAAATCCAATTAATAAATTCAAAACATGATTCATAAATACACAAATCCAATTCATAAATTCAAAACATGATTCATAAATACACAAATCCAATTAATAAATTCAAAACATGATTCATAAATACACAAATCCAATTCATAAATTCAAAACATGATTCATAAATACACTAATCCAATTTATAAATTCTTTAGAATGATCTAGCTCCATATGTCACAGACCCATCATTTGAATCATGCTAGTTCAAACTTAAAACCTTTGTAATGACGCTCCTCAAAGATGTGGAGTTTAAATTTAAATCATATAAAAAATACATACAAAATACATACAAATAAAATCTATGACAGAAGCTTTCTTAAAGTTCAACAAAACTTTTTATAATTGTTTCACACACAATATTTAAACATAAAAAAATGTATATAAATGAACCATCAAACCACTCATACTATATATCTACAGTATCTATATACTGTTCACTCATCGGCCACATTATTAGTTACACCTGTCCAACTGCTCCCTAACGCAAGTTTCTAATCGGCCAGTCAGATGGCAGCAACTCAATGCATGTAGGCATGTAGACATAATCAAGACAATCTGCTGCAGTTCAGACCGAGCATCAGAATTTGTATCTTTATTGGAATGATGGATTTAAGAAACCAGCAAGCTATGTTTGTATCTACATAACTCGCAATTGGCTAAAGTTGGTTTTACACACTCCATATTAGTAATGGATTATTTGAGGCATGTAAAGTTAGCCAAACACACAAACACATCATGAAACACACCCATAGCCACTGCCCCTAATAAACCACCCTTTTTCCATCACTTTAATGCTTTTTAACTTTATATTTTCAACCTCAGTCAACTGGAGTTTTTATTAAAGCTTTATGTTCCATGGTGTAATTGTCAGAAGTGCATTTCAAATGTCTTTTCTTGCAG
Seq C2 exon
TCGATCATAACATAAAACCCTCCGAGTTCCTCTTCACTCCAAGCAAACCTCAGGACAAGATGAGCTTTGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000014670:ENSDART00000014183:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0175512=Glyco_transf_25=PU(1.1=8.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTACAGATGTATGTGTGTAACAGA
R:
TCAAAGCTCATCTTGTCCTGAGG
Band lengths:
190-1886
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]