GgaINT0011647 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9173085-9175887:+
Coord C1 exon
chr20:9173085-9173169
Coord A exon
chr20:9173170-9175773
Coord C2 exon
chr20:9175774-9175887
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
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]