GgaINT0011670 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9199914-9201710:+
Coord C1 exon
chr20:9199914-9200023
Coord A exon
chr20:9200024-9201551
Coord C2 exon
chr20:9201552-9201710
Length
1528 bp
Sequences
Splice sites
5' ss Seq
AAGGTCCTT
5' ss Score
1.62
3' ss Seq
ACCTTGGTCTTCCCACCCAGGTG
3' ss Score
9.98
Exon sequences
Seq C1 exon
CCAGTAAGAAAACCTTGACCTATTTCAATCATGACTACAAGGCTGATTTGCAGGAAGTCTCCTTTGACCAGCAGGAAGTGAAGAAGATATTCTATGGGAGCTTTCATAAG
Seq A exon
GTCCTTATCAATAGAGGGAGAAATGTAGCTCACGATCTCATCCACTCTGAGACTATTATGCCATCAATGTGCATTGTTCAAAGCGAGGAATGATTATAAGTGCTTTGCATCCAGATTGCCATGGAGTCAGTGAACCTTTTTCATATGCTGAACATTTTAATTGTAGACTTTACAATTATATAGGTTCATCCTATGTGTAAGACACGTTTCCCACATATTGATTGCTTCTTAGAATGCACTGCATGTTTATGCATTTTTAAAGTGCTAATGAGGATGGGTAAATTATAGTCACACATGGTGGCCATTATTTTTGCATATAATATGTGGTAGCAACATGAAATGGCATCAAAATAAAATACACAAAGTGTATACCAAATTTTTCCTTTTACATGGTGTGCATTTGCCATTTCAGTACTAATTTGTATCGCATGTTTAGATATTTGCTTTACTAAAGATACAGCCTCCCTGCACAAATCATATAATTTACTGTATGGGAACATTTTATGAACTGTGCACTCCTCCAAATCCTTCCCCTTTATTATTTCCATCCCCAGCCAGTTTATTTATGGGCATGTGCCCTCATTCCCTTCTGGTGTGATGTGCTGGTCCCCATGACACACAGTTATAGAGAAAAGCTCAGGCTTGTTTTCTGCAGAACCACCATCTAGGAACTCAGTTCAAGTCACCCAGACCCCTCAAAACTGAATGAAATCTGTGAAATGTAATTGTTTCGTGTTAAATTTGTGCAAGAAAAATATTCTTTTCCCCCAGACATCATTACCATTATCATTACCATTGCTTCAGTCATAGTACAGTAATGCTGCGTCTGGAGAACTGCACTAGAAAGTGGTAAGAGGAAAGGCTTCAAGTACCTCAAGCCTTGGAGTCTCTTCCTTACTGGGGGAAAAAAAATAGGGTTATTTTTATTACAGTATAGTTTGGATTGGCTTCCCACAAAGTAAGATGGACACCATGAGGGAGTTGTTAACTGGAATGGACTGAGATGGAGAGAGTTATAGGAGAGGTCTCCTGGCAGACTCCTTCCCTTTCCCCATAGGAGCTCTTATTTTCAGGTCTTGAAAAAAAACAAAAAATTTGGAACATCAAATATTTTTTTTATAATTTGGGCATTTGGTGACATTTTAGTGCTGGAGGGAAGGAAAGGATGAAGTCTCATGAGAAATCCATCTGATCTCTTATAACTTTTGGGGTTTTTTTTGGCTGTCTGTATCCTCAGAGCAAAGGTATTCCACCCAGATGAGCAATAAGCTCTTTCTAACAGTATTTACATTATACAGCTGGTTCTGAGAACTGAATTACTCAGAACTGGGACTCCAGAAAGGCTTTGCCCAAGGAGAGCTGAGCTACAGCAGGGAACCACCAGGGAATGGTGCTGCTCACTCTGTCCTTTTGCTCACAGAAACCACATCATGTGTAATAATACCAGCACCAATCTGGGAACTGGGCAGAAGGTGTTTAAAAGCTCCCTGCCCCATTGCAGAGGTCCAACCTTGGTCTTCCCACCCAG
Seq C2 exon
GTGCACCTTGCAGTGAGCCTTTTCAAGATCAAGCTCTATCTGGACTGTAAAAAAATAGCAGAGAGACCCATCAACACCGTTGGCAGCATCTCCACCGCTGGCTTCATCATGCTGGGAAAAGTGACGCGGACCAGAGGGCCCAGGAGTGGATCAGCATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:25
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=0.132
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:
CCAGTAAGAAAACCTTGACCTATTT
R:
CGATGCTGATCCACTCCTGGG
Band lengths:
269-1797
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]