GgaINT0011655 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9181686-9183340:+
Coord C1 exon
chr20:9181686-9181850
Coord A exon
chr20:9181851-9183167
Coord C2 exon
chr20:9183168-9183340
Length
1317 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ACCGTGTTTTTAATTCCCAGGTA
3' ss Score
10.32
Exon sequences
Seq C1 exon
GGGTGAAGAACGCGGATGAGGCTGAGCTGAAGCAGGTGGCCTCAGAGCCACTGGAGCTGACGGTGTACAACGTGCTGGACTTCCCCCTGCTCAGCTCCCTGGTTGGCAGGCTCACCCGGGTCCTCTGCACCAGGATCAAAGAGAGGAGCAGCAAGGAGAGTGCAG
Seq A exon
GTGAGGTGAAACCTTGGTGAAGATGAGCTTTCTCCCGTTTGCCATCAGCTTTCCTTGCCATTAAAAAATCTCCTTTCTCAACTTTCTCATACCTTTCCCTCCATGAGCTCCACCACCTCCTCAGCACCATCTGACTCTTCCTTCCTGTGCTGATCTCCTTACTCGGAGCTATTGCTGCCTGAACACAGTCCTTGCCAATGTTTTGGCCAGGTCCAGCTGTGATCTCGGTGTTTACAAGACTCTCTGGATGCAGCTCTTCTACCCTCAATCCCTGCTGTTGTGAACAAGCCATGGAGGGACTTGCAGGTGTTTCCATTCTCTTGCTCTTGATTTAGATATCTGCTCTTATCCTTGCCAATACAGGCAACAGCCATCCTCACCAGGGCCTTGGATACCTCTTGGTGGCTGTAAATCACTCCATGGCAATAACTAGCATTGTAGGGAACAGGAGGCTTCTATTCTACATTTTTGTTATTCTAGCATGTGCAGAATGCATTGCAATCATTTTCTCTCTGCATTTCTTTCAATCAACAGGAGGAATTCAACACACAAGAGCTAAATTGAGAATATAGTAGTTGTATGGAAGAAATCTGGAAGTAGGAAGAGGAGACAGCAAAGCATCTAAACACATCTCTTTTCCTCCCACTTTAAGTAATCTCCAAGGCATCTTCAAATCAAAACCAAACAGTCTATTTCTTTTCTCTTTTTTCTTGCTGGAGGGCAGTTTGCATGATGTACAAGAGAGTGAAGAACGACTCCAGATGTTAGCTTAGATCCTCAGGAGAAATATCACGTACACATTTCCATCTCTCTCTTCTCTCAGACTTGCCTAGGGAGAATGGGGAAGACAAACTTTCAAGCATACATTTATTTTAATGCTCTGAGGATAGACATAGACATAATTTGATTCATTCTTGTTAATTTGTACCTGTTTGATGTAATTGGACATCTTTTTACAGGTTAGGTTAGCCTAAAGAAAGATGGTTACATAGAAAAAGAAGCGAAAATAACTTCTGGTTCTTTCTGACAGATCTTCGTAACTGAAAAAAAGCTGGGTTGTGTTTTGGATTCAGGCAAAAATGCATATTTCTGTTGAAAAGAATATTCCCAGCAACCAGAAGAACACACAAATTATTCTCTATGGAGAATTTATATTCTCTGTTTGCTCAGTTCTTAAATATTTATTTTACAGCAGTATGGAACAGCTTCTCTGCTCTGTAGGGAAGGGGACTGCAACTGGATTTAAAAAATGGCAGTCGTATTTATGAGCCAGAAAGTATATCTGGTAGGAGAAGTAACCGTGTTTTTAATTCCCAG
Seq C2 exon
GTAGAGCTGTGAAAGATATCCCTACAAATACAGGTCCAGAGCTGAGCCCGACAGACCTTAAAATATCAGCTGTCACTTCTAAAAGCATGCACTTGGCCTGGAGTCCTCCTCTGAGTCCACCAAAGAAGTACCGGGTTGTGTACTATCCATCAAAGGGCGGCACTCCCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.054 A=NA C2=0.276
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=66.1)
A:
NA
C2:
PF0004116=fn3=PU(54.4=74.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAAGAACGCGGATGAGG
R:
CTTGGGAGTGCCGCCCTTT
Band lengths:
334-1651
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]