DreINT0050606 @ danRer10
Intron Retention
Gene
ENSDARG00000073974 | colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:ZFIN;Acc:ZDB-GENE-070720-6]
Coordinates
chr3:52470631-52472897:+
Coord C1 exon
chr3:52470631-52470763
Coord A exon
chr3:52470764-52472769
Coord C2 exon
chr3:52472770-52472897
Length
2006 bp
Sequences
Splice sites
5' ss Seq
GAGGTCTGG
5' ss Score
2.59
3' ss Seq
ATATGTCTTGTGCAACACAGATT
3' ss Score
4.8
Exon sequences
Seq C1 exon
AGCTATGAACGTCAGTGAGATCCATGCTTTAGGAATACACATGCTGCCTGGCTACAGTGACCCTTATCACGGCAGACCTCTCACTAAAGGAGAGCTGGGCTGCTTCCTGTCCCACTATAACATCTGGAAAGAG
Seq A exon
GTCTGGCACACATCCCTGTTTGTTGTTTGGCTACAAAATCGCTGCATTAGAGTCAACTGCTTGAGAAAAGTACCATTCAAAAGCCTAGGGAAATTTTTTTATAAACTGATCTGTTCTCAGAATAATGCAGGAATTAAATTGTGAAATCAAACAGTAGAGTATTTCTCTACAAAGCCTTGCTATATTGTTGTATTAAGGGCGACAGGAAAGATGCAAGTGTCTTTGCTAGTTTCAGCAGGGTGCTGGTATCTTTTTCACATCTTGCACCTTACAGATTGTTGACCTGATTCCATTTAAATTCTTAGATCATTTTAGGACCATGATGACAAGCTGTACAATGATTTCTCAAACAGTTTATGTATTACTGATCAACAAAATTGTTGACATGTTGCTAAAATTTAAGCCTGTATTTCTGCATTTCTTTGGTAAATCTGCAGCATTACTCTCAGTGTTGGGCACATTCCTTTAAAAGAGTAATCAGTTATAGTTTCTAGTTACTTCTCACAAATAGTATCCGAGTTACATAATTATGTGCATCTGAAAAGAACATTCCACTTTTATTAATAATAGGCAAATTTTACAAGTCCTCTAAAGTGAAATGTCTTAGTTTTACAGTTTTGAATCCATTCAGTCGATCTCTGGGTCTGGTTGGAACCTTTTTTAGCTTAGCTTAGCATACATCATTGCATTAAATTAAACCGTTAGCATCTCACTCAAAATCAAGTTTTGATAAATTTTCCTAGTAAAGCTTGACTCTTCTGTAGTTCTTTCTTGTACTAAGACTGACAGATGATTAAATGTTGCAGTTTTCTAGGCTGATGGCTAGTTACCATACTCTCATTCTGGCTTAATAAACAAGGATCTTTGCTGCCATACCAGGCCTGCTGCAGGCACAACAATATTATTCCCCTGTTATAATATTATTATATTATATTAATATTACAATATTAATATAACAATATTCGACAGCCATATCACCCTGCAGCCCAAGACCGGTTACTCACTGAAGCTAAGCAGGGCTGAGCCTGGTTAGTACCTGGATGGGAGACCACTAGGGAACACTAGGTTGCTGTTGGAAGTGGTGTTAGTGAGGCCAGCAGGGGGCGCTCAACCTGTGGTCTGTGTGAGTCCTAATGCCCCAGTAAAAGTGAAGGGGACACTATACTGTCATTGGGCGCCGTCTTTCGGATGAGACGTTAAACCGAGGTCCTGACTCTCTGCGGTCATTAAAAATCCCATGGCACTTCTCGTGAAAGAGCAGGGGTGTAACCCCAGTGTCCTGGCCAAAGTCCCTCTATCGGCCCTTACGATCATGGCCTCCCAATCATCCCCTCTCCACCGAATTGGCTCTATCACTGTCCCTCCACTCCACCAATAGCTGGTGTGTGGTGAGCGCACTGGCGCCGTTGTCCTGTGGCTGCCGTCGCATCATCCAAGTGGATGCTGCACACTGGTGGTGGTGTGGAGAGACCCCCCCTCATGATTGTGAAGCGCTTTGGGTGTATTGCCATACACAATAAATGCGCTATATAAATACACACATTACATTACATTACATTACATTTATATTATTATCCTACCTAGGGACTATTTTCAGGTGCTGCATGATATCATTGTGCCAGCTGCAGCCATGGTACAGCAACAAAGTTCCTTGTTTATTATGCTGAAATGAGAGTATAGTAACTAGCCATGTTGATCTAAACCAGTGTTTCCCAACCCTGTTTCTAGAGGCACACCAACCGTACATATTTTGTCTCCCTTATCTGACCCATTCACTTCTGGTTTTGGAGTCCCTTCAAATCTTATGACGAGTTGAAAACTCAAATGTTTAACTCTGGGTGACTTTTAAAATGAGCCTATTTCCTTAGTGTTTCTTTAATATTTAATATTTAAGACAAAATCCTATGTTTCTCATGGAACTTGTTACTGTCTGTGTACCGCTACTGTTAGATTAGGACCTTGTGGGAAACTCTGCAAACCTTATAAATATGTCTTGTGCAACACAG
Seq C2 exon
ATTGTAGATCGAGGATTGAAGACCTCGCTAATTCTTGAAGATGACTTAAGATTTGAGATTTTCTTCAAGCGTCGCCTGCAGAATCTGTTGCTTGAGCTCCAAAGTCAGAGTCTGGACTGGGACCTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000073974:ENSDART00000154410:9
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:
PF0175512=Glyco_transf_25=FE(23.7=100)
A:
NA
C2:
PF0175512=Glyco_transf_25=FE(22.6=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]