GgaINT0011679 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9208936-9209424:+
Coord C1 exon
chr20:9208936-9209007
Coord A exon
chr20:9209008-9209388
Coord C2 exon
chr20:9209389-9209424
Length
381 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TCCTTTTGTTTTCCTTGCAGGGA
3' ss Score
12.31
Exon sequences
Seq C1 exon
GGTTTCCAAGGAGTGACAGGCTCCCGGGGCAGCAGCGGAGAGAAGGGACCTCCAGGTGATGTTGGGCCAACA
Seq A exon
GTAAGTAACTGAGCGTGGGTCTCAGAGAAGGCCAAGGCAGGAAATCATTGCGTGTAAGCAAGCTGCTCCCATGGTAGTTCTTCCTCAGCATCTGAAGGAGAGTTTAAATTCACACTCACCCTTCACATGGATGTGTAAATCCTGACCTTATATCTGTGGAATATCCTTGTTGATGGTGTTCCAGCACCTTAAGCACGAACAGAAAACATTCCTATGAGCTCACAGTACTTTTAGTCATTTTCATAAGGTCAAGGGAAGTACAAGTGTGTGGGAAACAAATCTTGGGCTCCACGTCCCGCTGATGTAACCTGCATCCCCACTGACCTTCTGCTTTCTCCTGCTCTCCCTAGACCGTGACTTTTCCTTTTGTTTTCCTTGCAG
Seq C2 exon
GGACTACCAGGTCCAAAAGGAGAAAGAGGAGAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(38.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.3=100)
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:
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]