GgaINT0011664 @ galGal3
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
NA
Coordinates
chr20:8835824-8836705:+
Coord C1 exon
chr20:8835824-8835966
Coord A exon
chr20:8835967-8836575
Coord C2 exon
chr20:8836576-8836705
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
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
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]