GgaINT0050802 @ galGal4
Intron Retention
Gene
ENSGALG00000003923 | COL6A3
Description
collagen alpha-3(VI) chain precursor [Source:RefSeq peptide;Acc:NP_990865]
Coordinates
chr7:4758719-4759961:+
Coord C1 exon
chr7:4758719-4758868
Coord A exon
chr7:4758869-4759343
Coord C2 exon
chr7:4759344-4759961
Length
475 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CCCCATCTGTTTTTTTAAAGCTG
3' ss Score
8.78
Exon sequences
Seq C1 exon
GTCTCACATCAGGTTCTTTGAAACAAGGAGAACAAAAAGGGAAACTGAAACAAAAGAACACAATGAGGAAGCATCGGCATTTGCCCCTTGCGGCAATACTTGGCCTCCTGCTCTCAGGCTTTTGCTCAGTGGGTGCCCAGCAGCAAGCAG
Seq A exon
GTAAGACGAGACCCATTACTGACCACAGTCCTCCGCGAGCACACTGCTCGCTCGCACTGAGATGTTTGCACCGTTTGGTTTTTAATGTGCATGTCGATGGTACATTGTGGTTGACCTCCTGCTCCTCCACTCCTGTTGGGCTGACCTCAGAGCCTGGACCTTCCCCAGCACGTCGCTAGCCGGCGGGCCAGCTCCAGGGTGCTCTGCGTGGCCGGGGTGCGGGATGTGGGGCTTTGCCCCAGCGTGGCCCCAAGTGGGTTTCCTCCAGGGCAGGGCTGTTCTGGCCTCCTTGCATGCGTATGAGCGTGGGAAGCAGAGGGGAGACACGAGAGGAGCTCTGTCACCGACCCACAGGGAGCTGCTGGGTTTTTAGGAGGTGCCGGCACCCTTTGGAGTGGAGCTCATGGCACTGGGTTGAGGAGGAATGCTTGCGCTGACTGCTAGAAAATCCTAAACCCCATCTGTTTTTTTAAAG
Seq C2 exon
CTGTCAGAAACGTTGCCGTGGCTGATATAATATTTCTAGTGGATTCCTCTTGGAGCATTGGGAAGGAGCACTTCCAACTCGTTCGAGAGTTTCTGTATGATGTTGTAAAGGCTTTAGATGTGGGAGGAAATGATTTCCGTTTTGCACTGGTCCAGTTCAGCGGAAACCCACACACAGAGTTCCAGTTAAATACGTACCCCTCTAACCAAGATGTGCTCTCCCATATCGCGAATATGCCTTACATGGGGGGAGGCAGCAAGACTGGAAAAGGATTAGAGTACCTAATCGAGAACCATCTCACTAAAGCTGCTGGAAGCAGAGCGAGTGAAGGCGTCCCCCAGGTTATTATAGTGTTAACGGACGGACAATCCCAGGATGATGTGGCTCTGCCATCATCTGTCCTTAAATCGGCCCATGTAAACATGATTGCGGTCGGCGTGCAGGATGCGGTGGAAGGGGAGTTAAAGGAGATAGCGAGCCGACCCTTCGATACCCACCTTTTCAACCTAGAGAATTTTACCGCTCTCCATGGCATAGTTGGAGACTTAGTGGCAAGTGTCCGTACCTCCATGACTCCAGAACAGGCTGGAGCCAAAGGACTGGTTAAAGACATCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003923:ENSGALT00000006250:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.006
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=WD(100=85.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGGAAGCATCGGCATTTGC
R:
CCTTTTCCAGTCTTGCTGCCT
Band lengths:
358-833
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]