DreINT0007395 @ danRer10
Intron Retention
Gene
ENSDARG00000058270 | COLGALT1 (1 of 2)
Description
collagen beta(1-O)galactosyltransferase 1 [Source:HGNC Symbol;Acc:HGNC:26182]
Coordinates
chr1:57286405-57288287:-
Coord C1 exon
chr1:57288177-57288287
Coord A exon
chr1:57286523-57288176
Coord C2 exon
chr1:57286405-57286522
Length
1654 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGT
5' ss Score
8.94
3' ss Seq
AATGCATGCATCTTTTGCAGTGT
3' ss Score
7.19
Exon sequences
Seq C1 exon
GGTGGCCACAGATCATAACTCCGACAACACCACCGAGATCCTGCGCGAGTGGCTGGTGAACGTGCAGAACTTCTATCATTATGTGGAGTGGAGACCTCAGGACGAGCCCAG
Seq A exon
GTCAGTCTTCATGCACACACTGAAGTTATTTCAGATGTTCTGTTCAAGACTAAACTAAGATTTAGTCATTTTGATTGTGTTTTTCCTCATTTTTTGTAGCTTTTTAGAGCCAATTTAGTTCAGAAATGTTTACTTTTAGTTGTATTCATTGTATTTTTAATTTAAACAACACGAACAAGTAATATTTTCTTGATGAACAATTAGTGACGAGTAATTTCTCGTATCTATTTTAGTTTTTTCAGCTTTTTTTTTTCCTTTGTTTCATTTGAGTTACAAAAACACTTTATTTGTAGTTAACTAAAATTGATTTTACCAAGCCTGAATTCATGGTTTCTGCAGGTTTCACAGTTAAATTTAAGATATTTTTAAGACCATTATGAATGGAATTTTAGACCCATAAAGGGCAAAAATGTAAGACATTTTTCAAATGACCAAGATGGAAAAGATTTTTTATTTGCCCTATCAATTAAAACATTTATAATTGAATACATTTAATAATACAATAATACCTTATTATTAAAAAATAAAATATTTTACATTACATTTTTTAGCAAAATATTTTAAATATCGTGTAAAAACAAGCAAGCTCTAGTTGTATCAATACACGTTTTACAACATAAACAATCTTTAAAATAAAAGAAAAATAAACAAATGTTTTGAAAGTTTTAAAAACTATAATAAACTAAATATGGACAACAATCTGTCCAGGTCAGTGTCCTCAGCAGCAAATACATGGAGACATTGAAACAAATATTATTGTGAGGAAAATGATTAAACTATTATGATAAATAAAGTTAAAAATGACCTTTTTAAATAAAAAGTTCAAAATTGTATAGAGAAGATTGTTGATTATTGTATGGGTTTTGGCCAGATTTAGTAGAAATACATGGAAAGGAAAATTAAGACCTGTTTCAAAAAGATTTAAGACCTACAGCACAACATTTCAGTACATTTAAGACTTTTAAGGCCTAAAATTTGGATTTTAAGATTTAAGGCTTTTTAAGACCCTGCAGAAACCCTGGATTTAAAAGCTGAACTTGTTTAAACAGCAGATATGTTTGCACATCTTATATAAAACATAATTTTGTGGTCATTAATAATGTAAATTTGATTAGTACATATGTACACTATAATTTTAGACTCATAAAGGGCTAAAGGCTGAGAAATTTTTCAAATGGCCTAGATGGAAAAAAAATATACTCGCCCTATAAAAAAATATTATAAATCTAATACATTTATTTAATACAATGGTAATTTAATAATGATATTTTTTTTTTTTAGGAATTCATTTCTTAGCAAAATATTTTTAACTATTGTGTAAAAACAAGCAAGCTCTACTTTTATCCATACTCTTTTTCCAACGTAAGTGTAGTTTATTTCTAAACTAATTTCCAGAGGATCACGTGCTTATGATTGCTTGCAGCCGGTGCTGCATTATTCAATTTAGGATTGACCAATCAGACACTATAAATACCCTCAGTTCCATATAACAGCTATCTTCGTTTGGAAGAAAATTCAGCTTTACATCTTATAAATTAATGACATTTTACTATATATTTACATGGAAAGCAGCTGTTTGACGCTGTACTGTTTTTGCTGTAGTTTTTTGGGGGATATTTGGCGAATGACCTCAGAATGCATGCATCTTTTGCAG
Seq C2 exon
TGTGTATGAGGGTGAAAGCGGCCCGAAGCACTGGACGAATCTGCGATACGAGCACGTGATGAAGCTCCGGCAGGCGGCTCTGGAGACGGCACGCGAGATGTGGGCCGACTATTTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058270:ENSDART00000081122:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.050
Domain overlap (PFAM):
C1:
PF050639=MT-A70=FE(33.6=100),PF137041=Glyco_tranf_2_4=FE(35.6=100)
A:
NA
C2:
PF050639=MT-A70=PD(30.9=85.0),PF137041=Glyco_tranf_2_4=FE(37.5=100)
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:
GTGGCCACAGATCATAACTCCG
R:
AAATAGTCGGCCCACATCTCG
Band lengths:
224-1878
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]