DreINT0050610 @ danRer10
Intron Retention
Gene
ENSDARG00000014670 | colgalt2
Description
collagen beta(1-O)galactosyltransferase 2 [Source:ZFIN;Acc:ZDB-GENE-070222-1]
Coordinates
chr8:19343601-19345218:-
Coord C1 exon
chr8:19345108-19345218
Coord A exon
chr8:19343719-19345107
Coord C2 exon
chr8:19343601-19343718
Length
1389 bp
Sequences
Splice sites
5' ss Seq
ACGGTTGGT
5' ss Score
6.35
3' ss Seq
TTGTTTATTTGTTTATTAAGGTC
3' ss Score
8.17
Exon sequences
Seq C1 exon
GGCTGCAACAGACCATAACGTGGACAACAGCACAGCCATGCTGAGAGAGTGGCTGAAGAACAGGCAGAGCAGATATCACTATGTGGAGTGGAGGCCCATGGAGGAGCCACG
Seq A exon
GTTGGTTGAAAACATCTTGTTCCAAAACAGATCAATAAGCACTAATCAAATCACTTCCAATCCAATTAGCACTAATAGCTGTTTATGTCAGGACTTTGTGGCAGTTTTTCTGAATTAAAGCATTTCCAGAAGAAGGATTAAATAAGTGTGTTTGCTCTGTTGACATTTATTCACCTTCCTATTTTTTCCAGTATTAATATACTCTCATTGGCCACTTTATTAGGTACACCTTACTAGTACAGGGTTGGACCACATTTTGCCTTCAGAATAGCCTTAATCCTTCATGGCATAGATTCAACAAGTTACTAGAAATATTTCTCAGAGATTTTGCTCCAGTTTCCCAGAGATTGCAGCCGGAAAAGCATCCACTGCGTAAAAACAAATGCTGGATAAGTTGGCGGTTCATTCCGCTGTGGCGACCCCAGATTAATAAAGGGACTAAGCCAAAAAGAAAATGAAGGAATGAGATTTTGGTCCATATTGACATGTTAGCATCACACAGTTGCTGCAGATTTGTTGGCTCCACATCCATGATGTAAATGTCCTGTTCCACAACATCCCAAAGGAAAAAATCCCAGTAAATCATCAGTTTAGCCTGTCTTGCACTAATAACCATGCAACATTCAAAGTCACTTAAATTACCTTTCTCCCCCATTCTGATGCTCAGTTTGAACTGTAGCAGATCATTTGAACATGTCTACATGCCGAAATGCATTTAGTTGGTGCCATGTGATTAACTGATTCGAAATTTGCATTAACGAGCAGTTGGACTGTTGTACCTAATAAAGTGACCGGTAAGTGTATAAAGTGGAAATATTTGTGTACCTAACAGTTTAAACAAACATGCAAAAGAAGTGTCATTAAACACTATATTTTGAGACTTTTGAACTCAAAAAAACTTGTAATGTAACTGTAATACAATTAATGAGAAAAAAGGCCATGTATTATTATAGGATTTTAAACCTGTATTTAACCTTAGAATGATTTCAAATTAAAAGTGTCTGATTTTGTCTGTCGTTTAAATTTAAAGGATTATAATCTTATTTAAGTGATTAAGGATTTGGAAAGTCTGACAGTAATCAGTGTTGAGTACTGCTGTAAGGTTAATCCTGCCAGGTTTAAATGTTTTGACGATGGACTGTTGGAAACATTCAATAGAAATTTAGTAAAGTAAATAATGCTGTCTGATCCCAACAAATGTAGTGTTCTTTAACTAAAATATACTCAGAATTAACACAAAGTGTTGTCGATATTTATCTAGGACAAATTATTTTAATATGAATGTAACATTTTCTAATCATCTAATTAAACAATTAAATTTAATTTTTCGATTTTAATTTGATATCAATCGATATTCATCGATATTTATTTGTTTATTTGTTTATTAAG
Seq C2 exon
GTCATACACAGATGAGTGGGGGCCAAAACACTGGTCTTCGTCTCGTGTCAGTCATGTAATGAAGCTCAGACAGGCAGCATTAAAGGCTGCAAGAGCTCGCTGGGCTGATTATATACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000014670:ENSDART00000014183:2
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=0.000
Domain overlap (PFAM):
C1:
PF137041=Glyco_tranf_2_4=FE(30.6=100)
A:
NA
C2:
PF137041=Glyco_tranf_2_4=FE(32.2=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:
GGCTGCAACAGACCATAACGT
R:
ATAATCAGCCCAGCGAGCTCT
Band lengths:
223-1612
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]