GgaINT0011662 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9187510-9188861:+
Coord C1 exon
chr20:9187510-9187652
Coord A exon
chr20:9187653-9188728
Coord C2 exon
chr20:9188729-9188861
Length
1076 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGG
5' ss Score
8.98
3' ss Seq
CATTTCTTGCCCTGCTGCAGCTC
3' ss Score
7.16
Exon sequences
Seq C1 exon
TGAAGGTCCCCCCGCCGCGGGCGCTGAAGGTTTCCGAGCTCTCTGAGAACAGCCTCCGGCTGCACTGGGAAGCTGTCGCTGCCTCTGATGTGGTTGTCTATCAGATCAAGTGGAGCACAGCTGGTGGAGAGAAGCCTCAGGAG
Seq A exon
GTATGGACCCACGTACAGCCGGGTTGGGTTTGTGCCTGCTCGATGGATATTGGTTGGGTATTAGGACAAATTTATTCTCAGAGAGAATGATCAGGCCCTGGAATGGGCTGCCCAAGGAGGTGGTGCAGTCACTGTCCCTGAAGGTGCTCAAGAAAAGGGAAGATGTGTCACTGAAGGACGTGGTTTAGTTGGCATGGTGGCGATGGGCTGTTGGTCCTACTTCATGGTCTTAGTGCTCTTTGCAACCTTAATGATGCTATGAGGGCTCTGTGCCCACCTGCAAGAGTGGCAGGGTTGCAAATCAGTTTGGGTTCATGCACTCAGGACCTTCAGGTCTAAGACAGGATCTGTCCCACACTGGCTCTGCTGAGTGCTGTAGTCACCTTGAGTGCTGGAAGCAGGAGGGACAACGGGGAGGCAGGTTTGGAGTCTTACAGGCTCTGGGAAGATTGCAGAAGTGCTCTGGAAAAACTCAAGGATGAAATTCAATAGGGACAAACAAAGTATTAAGCTTAGGCAGGAATAATTAAAGACAGGTATACAGGATGTAGAGCAAACAGCTAAGAAGCGATTCAGTAGAAAAAGATCTGGGGTTGCAGAGAATCACCAGCCCACAATGTCAAGTCGTTGTGGAAAAGGCAAGTACAATAGTCAGGTATTTGTAGTGGTGGTGAGTCCTGACTGCTCTGGGGATAATACTCCTCAGGAAGGGTGAGGTGTTACTGATGAGAACACAGAGAAGATTGAGCAGAATCAGGGCTGATGTAGATGAGAGCAGAGATATTTCATGCTCATAGCAGGCTGACTGCCTTGTGCCAGCAACTCTATGTTGTGGGACAGAAGTAGCTGTTAAATACAACTGGCTAGCAATGCATAGGCATCTACTCTGCATTCATTAGGGCTGGAAATTTGCCTTTGCTTGGATTTGTGCAACCCACAAGAGTCGACTTTGTCCTCAAAGCCCTGTGCTAACTCATTTGTGCCTGCAGGCAGTCTGTGAGCCAGACACTTGGATGGCATGAACTAGCTTAGGGAAGCCTGGGAATTCGACTGACTCATTTCTTGCCCTGCTGCAG
Seq C2 exon
CTCTCCATCGCTGGAAATGCGGCAACTGCCGTCCTGCCAGGCTTGCAGAAGAACACAGACTACAAAATATCCATCTGGGCCTACTACAAAGATGGTGCTCGAAGTGACACAGTTTCCATTCAGCACAGAACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.267
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.7=91.7),PF0201812=CBM_4_9=PU(23.9=54.2)
A:
NA
C2:
PF0004116=fn3=PD(43.9=80.0),PF0201812=CBM_4_9=FE(40.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGAAGGTTTCCGAGCTCTC
R:
TGGTTCTGTGCTGAATGGAAACT
Band lengths:
254-1330
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]