GgaINT0011671 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9201552-9203645:+
Coord C1 exon
chr20:9201552-9201710
Coord A exon
chr20:9201711-9203567
Coord C2 exon
chr20:9203568-9203645
Length
1857 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
GCCTCTTCCCTTCCCCACAGTTC
3' ss Score
12.4
Exon sequences
Seq C1 exon
GTGCACCTTGCAGTGAGCCTTTTCAAGATCAAGCTCTATCTGGACTGTAAAAAAATAGCAGAGAGACCCATCAACACCGTTGGCAGCATCTCCACCGCTGGCTTCATCATGCTGGGAAAAGTGACGCGGACCAGAGGGCCCAGGAGTGGATCAGCATCG
Seq A exon
GTGAGTGCCCGGAGGTGCCTGCTTTGGAAATTGGGGGGTTAAATGTGAAGCTAGTTGGGCAGATGGAGGGTTGTGCCAGCCTCACCGTCCTCGCTCTGACAGCCTCCAACAGCAGCTGTGACGCAGGGCTGTGTGCTGATCCCACTGATCTCTGCGAGTTAATGAGCTTTCCTGGTGTGGGGATTCTCCTCCTCGCCTCCTACCTGGGTTTGAGGTCTGGGCTCAGGGCCCAGTACTGAATGCTGGAAGCACAGACCCTGCCCTAGCAGGCAGCAGCAGGCAGCAGATATAGGGAACTGCTTTGGAAGAGAAGGTAGTGCCATCAGCCCTCACTGAGTGGCACTGGGAAATGCCAGGTCTGGAGGTGCCTCAGTCTCCTGTGTGCTTGGGCTTGGCAAATGGTGGCCAAATACTCTTCAGTACAGGGGCTCCTTGTCAGCTGCTGTGTGAATTAAAGCAGTCCAATGCTCAGTACCAGCCTGCAGGCACTTCCATGCTGCACTGCACAGCACCCTGCGAGAGGACAGAGCAAGGGAAGTGTGGGTTCCACGCCGTGCCTTGCAACAGCCCCATGCATCACTTAAAATGCAAAACCACCCCTGCATGGCATTGCTCAGGAGCCTGCTGCCACGTTTCCTCCACAAAACTGGAATGTTAAATATGTGCAGAACGAGGAGGAATTGCTCAGTGAGACTGTAGGAAATCATTCATGACTGTGAAGCTTTTACTCCTGGGTTCTGCTTTTAGGTCTAAAAATGTAGAGGGAAACAGCCCAGCCACTGATTTGCAGCTTCCCTTGCCTCAGAGCAGTGCAGTCAGAACAGTTTGTCCCACCCCCAGCTGCCTGGTCCTGCAAAGAGCAATGCAAAAGTCTGGGGTGCACCAGGGAAAAGCGGGTATTGGAATCACCTGTGAGCAGTGGTGACACATGACAAACCAGGGCACAATGGGATTCAAGCAGTATTTTCTGAATATGTGCTGTGGCAGTTTAGATGGATCACAAGCCTGTCAGAAAAGAGCCTGAGCTCTCCCTCTCCCTCCCAAACTCTCCTTGCTCACAGCTCAGCCAGACAGATGCAGCTGACTAATGAGCAGCTTCGTGCTGCCTCTGCTCCTATTGCTTTTCAAGCCCAGCATAAGGCTCACGTCCTCCACAGCTCTGCTGCCCTTGAGAAGATGGAGCATCTCATTACTGCTTATCATGGAACCTCATTTAATTTGAGATACCTTTAAATGCTGCTTGGTCGAGGAGGCTCACCTGTATCTGTGATGCGCTCCTCAGCTGTGCAGCTTAAACGCATGGAGCAGAATTAAAAACAGAGGAGAAATGGTGCTAAGGAAAGCAAAAAAAAACCCCACCTCTCTGCCTCGTCTTCTGTTTTTGGTTTGCTTTGTGCAGTGTGTGCTGCTGTGTTCATCACGGAGGCAGTGGTTGGGAGGGATGTGGTGTAGGCAGGAGGGGTTCCTGGGAGGGAACACAGCTCTCCTGGGAGCTGCTGCCACTTTTCCTCTTAGGTACATTCCTCTGAAGGGGGAAATGCAGACAGCAAAGTTTGTTTTCACGTTTTGACGGTGCTGAAGCCCAATTACCTGAGGACCTGCCTGCTGCCATGGGATGGTGTGAACAACCAGAGAGGTGGCTTTTTCAGGGGTGAGGCTGCAGGGTGGCTTAGCAGGGCACAGAGCTGCGGCTGCTTTGTGTGTCACGGCTTTTTTGGTGCAGTTACAGCTGGGAGGACCACACGTGGAGTCTGCCAAACCACCACTAAGCATTATTTTTAGCACATGGTGAGCTTTGGCGGTGCAGCCTGTGTGCCACTGCCACCTTCTCATCAAAGCCTCTTCCCTTCCCCACAG
Seq C2 exon
TTCCAGCTGCAGTCATTGCAGGTTGTGTGCAACAGCTTAGGGGCGGAGGAGGACCGATGCTGTGATCTTCCTGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.132 A=NA C2=0.077
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
ACCTTGCAGTGAGCCTTTTCA
R:
TGCAGGAAGATCACAGCATCG
Band lengths:
230-2087
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]