GgaINT0011680 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9209389-9210818:+
Coord C1 exon
chr20:9209389-9209424
Coord A exon
chr20:9209425-9210751
Coord C2 exon
chr20:9210752-9210818
Length
1327 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
ATTGTAATGCTTCACTTTAGGGG
3' ss Score
6.66
Exon sequences
Seq C1 exon
GGACTACCAGGTCCAAAAGGAGAAAGAGGAGAGAAA
Seq A exon
GTGAGTTTTCCTGGTGCTGTACGTCAAGCACTCGAAAGAGTGGATGTGGTAATCTGCTTGGCAAGCTATGCTTACATGTGAAGACCTTTACAGAGCAGAATAACATAATGTACCAAGGGCTCGTTGCTTTCTGTTCACCTGCACTGGCTGTTCTGACGGGTGTGAATAATGAGCTGCTTAGTACCAATTGTAGTAGCAAAGAAGAAAAGCCAATTGAAAATCCATCCTTTGCTGAGAAGTCAAAACCAAAACCACTCAGTTTCACTGAGGGTTTGTTTTGTTTTGTTTTAAATGTGTGGCATAAGGCTGGGGCTCACTTCTAGCAAACCTGTGCCACACTCGGGTACAGAGCCCCTGAGGTCAGGAAAGCAACGCTGTCTGTGAAGGTTCTTCTATTGTCAGAGGAGGTTTTGTTCATCTTGGCTTACATTTAAAAAGAAATCCTATATTTTTCTAGGAGTCCAAGTCTGCTTGCCAATATTCAGTTAAGTGAATTAAGCTTCAGACAGGCGCAAGCTGCTTTTCACAGACTGCTTTTCTTCTTTTGTTTCAAGTGAATGCCCCAGCATTATAATTTTTAACACCGTCCTCCTTCCATTTCCAACAGCTTTTCCTTTTCTATATATATAGATATGTATATTTCTTTTCAGTGGAACTTTCCTTTTTTCCTCCCTTGAGTGTAGTGCTAAGCTTTTGTTTAAGCTTGGTAATCTGCACGGTGGTCCACACAGAGATGGACAGTTTAGAAATGGTTCTGGAAGCATTCACGGTCTTCGCTATGAATTTTCATGAAGAGACTCATTTTTTAAGCAGCTTTTTTTGCACTTTTGTCCCTGCGTTACTAAAACTTTCCAAAGAAAAACCTCAGATGTCATTTATTTTGAGTTTAATAAGGATAAGAATCAATATTCATAAAAGATTGAGACAAAGATAGGATATTGTAATATCTGATTGCGTTAAATGTTTTACATATCACAGAATATTGAGTTATGCACTGCCTATCTGTTTTGATGAAATTTGAGAGGGAAATTTACTCTCCTTTTTTTTTGGTAGCTTCAGTAATTATATCAATTCAGTCTAGGCTTTTTGATGTGTGGGAGAGGAGCAATTATTGATGCTTCCCAATTACAGTTTTATGGTGTTGGAGCTTTGTAATAAATAAATCAAGAAAATGCATTTCATAGCAATTAATGTCTCAGTAACACCAGCTGACAGAAGGAAAGGGCAGAAAGCTATCCTGCATTGTGATATTGATCCTTTCTACAAGATATCGATGAAGACGTGAATACTTCCTTCTCTAAAACAGAATTGTAATGCTTCACTTTAG
Seq C2 exon
GGGGAACCACAGTCCTTGGCCACAATTTACCAGCTCGTTAGCCAGGCTTGTGAGAGGATGATCCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:35
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=0.826
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(18.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(8.3=21.7)
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]