GgaINT0011664 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9191977-9192858:+
Coord C1 exon
chr20:9191977-9192119
Coord A exon
chr20:9192120-9192728
Coord C2 exon
chr20:9192729-9192858
Length
609 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TTTTTTCCATCCTGCTGTAGATC
3' ss Score
10.14
Exon sequences
Seq C1 exon
CTTCTCGGAGCCCACCCACCAACCTCTTCATAGACTCTGAGAGCCCCACCAGCCTCCAGATCCATTGGAAGCCCCCCGAGGGCCGCATACAGCACTACAGAATCACCTACAGTCCTGTTTCTGACCCCAGCACCCAGCAAACA
Seq A exon
GTAAGTTCAGCTCCTTGGCAGGTGGGACAGAGGGGCAGTTTCATGGCTAACAGAGTGCTGTTCACTCCAATAGGGTTTTCCCTATCAAGAATTAGTTTGCTTGCGAATGAAACCAAATTTCTTCCTTTGGCATGCTGTCAAGTTGCTTTGTGAAGAAGGCTTCCTTCTGATTCAGGCTTCCTTCTGATTCACTTACTGGTGTCCATCAAAGCTGCAAATAACACAGCTTTCTCCTCTCCCTGAAACAGAGTGGGTAATTCCAAGAGGCAGAGTGGTAGAGGATAACTCTACTGCCCACCTGATTTGACAGGTTAACAATTAACCTTTCACAGTGAACATTGGCCACAGCAACCCAAACTGGCGACCATATTTTAAGGATCTTTTGACCCATCTACGAGGGGAATATTGAGGTCTTTACTTAGGAAAGCACTCTTCCCCTGGACACAATAGTTCTGATGGCAATGCATAGTCAGGCTTCTACGGTTTCCTTTTACCATTCCCTAATAAATGGGGATGCTGCCCTGGAACTCAGTGCTAGAAATCCTCAGAGTAGCCCCAGGGTGTGGATAAAAGCCAAACTCTGGGCTCTTTTTTTCCATCCTGCTGTAG
Seq C2 exon
ATCATGGCTTCTGGGAAAAGCAGCAGTGTGACCTTGCAGCCACTGCTGCCCGATCGAGCCTACAAGGTGACGGTTTCTGCCGTCCACTACACAGGAGAGAGTGAGAGCACAACTGCAACGGGTCGGACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.542 A=NA C2=0.409
Domain overlap (PFAM):
C1:
PF0201812=CBM_4_9=PD(33.9=77.1),PF0004116=fn3=PU(53.7=91.7)
A:
NA
C2:
PF0004116=fn3=PD(43.9=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCTCGGAGCCCACCCA
R:
GTCCGACCCGTTGCAGTTG
Band lengths:
271-880
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]