GgaINT0011647 @ galGal3
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
NA
Coordinates
chr20:8816272-8819074:+
Coord C1 exon
chr20:8816272-8816356
Coord A exon
chr20:8816357-8818960
Coord C2 exon
chr20:8818961-8819074
Length
2604 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
ACACCTCTCCTCCTTCCCAGGGT
3' ss Score
9.77
Exon sequences
Seq C1 exon
GTCCTGCTCACCATGCTGATTCGCACCTGCTTCTTTTTTGCCTGCCTGCCCGTGGCGAGCCACGTCTGGGGACGAGGGGGACAAG
Seq A exon
GTAAGGACCTCAACTGCACTGCTCTGGGGGGGCTCTGGGCTGGAACCGGGGCTGAGCTGCAGCCCTTCTGGTGGGGAAGCTCCAAGCAGCGTATTGCCGTATGTAAAGAGCAATAGGAGATCAGGGGGCCCATGCTGGGAGAGTGTCTCCATCCCACCCCACTCTGCAATGCCTGTTCTCATCTCTGGCAGCAGCTCAGCGTGCCTCTCCCTTGCACTGGGGATGCATTTCAGTCTGCGTAAGCAGGGAAGGGTGCTTGTGGGGTCTGCTAACAGAGCCTGAGTAACGGAAAGGAAAAATTGTTGCTTCTGTTCAGTGTCATGTCTGTCGTGCACTGTGAAACTGTGGAGCTACATGGTGATGTGTGACACCTGGGTAAGGGAGTACATGATGTGCATCCTCCTGTAGCATGTAGTGCTCCTGCAGTGCCATAAATGAGCAGAAAATACCTCTAGCACCTCACCATTTCCTTTCCACATTTCTATTCTGTATGAATCATCCATATGAGGGATCACCACAAGGTTTTCCTGAGAGGTGATGGCACATCACATTCAGGACTGACTTATCTCTGTGCTGTGCATCTTCCATGCAGCGTGTCTGGGCTTTGCTCCCCATCAGCTGGAGAGCAAGGTTACAGCATCAGAGAGCACACATCCAACACAGGGCAGAGAAACAGTGGGGCTTTCATGGCACCGGGCTTCATTTGCATCCAGCACATAATGGAGCTTCAGAGGATGCTGTCCTTTCTGATCTCTCTGGGGACATTCTTGCCTTTTTAACTTCTGGGCTCCTAGAGTGATAGCCAAGGAGCTGGACCACACTTGTCCAGAAGAAGACAGCTCCATGTTTCCTCTATGAATTCCCCTCATTGTTGCATGATCTTTTATCACTTCTCTTCGGCACGATTCCGAGATTTGATTTCGCCCCTCACCCCTCTTCCCCATGTTTTCTTTCTTCCTCTTCAAATTTCCATGGGGTGAGATGTGAATTTGAGCTTTGTTTCCCCAAAATAGTTGTCTGCTTTTTGGACAGCCCACAGGAAGTCTCTGCAAGGAGAGGTTGAGGCACAGATGCTGGGTTGAGCCAAGCGAGTCCTTGCTGCCAGCTCCCACTGCTTTCCTGGGCTGTGACTTCATGCAAAGATGTTGGGAGATGTCTGACACCATGCAAGACCAAAACAGGAACATGTGGAGTCCTACAGAACACACAGCGTGCCACGCTGAGCACAATGCTCCACATCACCTTAAGCTTTAATTTTGTTCATGAGTAGTGAGAAGGAGAAAGAATCATAGAATCATGAAGGTTGGGAAAGAGCTCCAAGATCCCCAAGTCCAACCCCAGCCCACCCCACTGTGCCCACTGCCCACATCCCTCAGTGCCACATCTCCATGGCTCTGGGACACCTCCAGGGACAGTGACCCCACCACCTCCCTGGGCAGCTGTGCCACTGCAGCACTGCTCTTTCTGGGAAAAAAATGTTTCCTAATATCCAGCCTGACCCTCCCCTGGCACAGTGTGAGGCCGTTAGCAAGACACTGGTAACAGCTGCCAACGAGGTGGACATTTGAGGTCATATGTTATTCCTATGCAGACAAAGGAGACACTTCCTCATTGCACATGAAGGAGCCTGCTGGAAAGGCAGCTGTAGGCGCAGGAGCAGGGAGGAGGGGAGGCAAATCTGCTGAGTTGCCATCCTACAGCTGGTCAAGTGGGAATGCTTCATATAGTGACATCTGTACGACAGTGTGGCTGTATCTCACTGATGGATCTCTGATTCAAAGGCTGACACGTGGGTTGAGACATTTAGCATGGCTTTAAAAGATCTCTGAGAAATCCGGAGCTGATAAGAGAATGTGCTCTTTCTTCTTTTTCCCTCCTTGTCTGATACTATTTTTTTCATCAGGATTTGTCATTTCAGTTCACTGATCCCTGCAGCAAACCAATGCAAGCTGGTGCCCGTGAGTTACGGTCCTGCCAGGAGGTGTTAGTTACACTTTATCAGGTTTTCTCTCCTCTCTCTTTCTTCTTTTTTTTCCCTTTCCTCTCTAAACCCAGCTGATCCTTGGAGCTTCCTCCTAAACAATCTTTCTGCATAAAGATGGCATTCATCTCCTGGGGACTTTCTGTATTTTTCAGCAGCTTGAGCTCATTGCAGAGCCTCATTGACTCCCTGTATCTATTCCCTTCCCTTCTATTTCAGACATCTGCACCACAACCCGTGCTGAAACCACAAACATGCCATGAAGGCTCCCAGTAAAGACTTGCAGTGCGAGAGGAGCGCAGAGAAACTCTCACTGCTTTGCTCATTTGCTCCTCATTTGCAGCAGCACATAATGAGGGCTCACCCAGAGAAGCTGCCCCTTAGCTTTGGATGGAGGGTGGATCTGCAGCAGTGGGTTTCCTGGTCCCATGGGCAGCAGCAGTGGCTGTGCAATGTCAGGGGATGCTGAGTGCTTGTATGGGATGATGAAGGTTCCCTTTGCATTGCAGCTGTCCCCATGTCTTTAGCAGAGGTAGCACATGGGGGGGTTTCATGCATGGGTGAGTGTGTGCAGAGGGAGGAATTGCACCCACAGCAGGATGGACACCTCTCCTCCTTCCCAG
Seq C2 exon
GGTCATCAGGCCGGCTGAAACTCACAGTCCTTTCAGAAGACAGGCTCCAGATGAAATGGAAAGAAACCGAAGGAAGCATCAATGGCTACAAAGTGCGGGTAAAGCCCATGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.103
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004116=fn3=PU(48.1=94.9)
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:
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]