GgaINT0046118 @ galGal3
Intron Retention
Gene
ENSGALG00000002552 | COL3A1
Description
NA
Coordinates
chr7:577742-578954:-
Coord C1 exon
chr7:578901-578954
Coord A exon
chr7:577796-578900
Coord C2 exon
chr7:577742-577795
Length
1105 bp
Sequences
Splice sites
5' ss Seq
CGAGTGAGT
5' ss Score
8.49
3' ss Seq
TGATTTTTTTATTATTTTAGGGT
3' ss Score
10.32
Exon sequences
Seq C1 exon
GGAGAACCTGGTGGTAAAGGTGCTGATGGCCTTCCTGGTGCAAGAGGAGAGCGA
Seq A exon
GTGAGTGTTTAAGCTTCAGTTTCTGAATTAAATTCATCTTGTCTATGCATTAAATGCGAGTAGAGTTACAGTGAATAAATACTATCTAGGAGAGAGAAAGTAGTAACCCAGTTGTATTACATTCTGGCTGTGTAAATCCGGTTTTGTAAGCTAATTTAGTCTTATTACTATTCCTTGTGATCATGGCCATTACAGCAGAAATAATAGAATTTTTGCAAGGAGAAGATGACAGTTAATGGAGACCAGGCTTTGGAGGGAAAGCACCAATATAAAAGTAGTAAAAATGTGAATTTCCTGGATGGAGCCAATTGAAGAGAAGTATTTCGGCAATACTGAAGTACAAGATGTTGTGATAGCAAAGGCTGTCATGCAGAATACTTGAACAGTTTACTATATATTTATTTATGTATCTATCCACAGCACATGCAAATTGTTGAACATGTGTTCAACAACTATACACAAGCAATATATACATAAAAATAATGAGAGGTAGCAAATAAATATATTAATGCAGGTTGTATGAATTGAAGGAAGGAGAAAAACGGATTTCAAAACGTAAGGCATGCATCAAATTCTCATGGAAAATACAATGGAGGAGTTGAACAACACTGGAGAAATCCTGAAGAAATATGGTCCACTTACCTATATATTAAATTCAGGGCAGTAAATAACTATCATTATACAACGGAAAGACACCTGTTGACCTCAGATGACTTTGTTTTAGGTTTACAGGGGAGGATCTGGGGAAATAAGAACTCACACTGCACTAAATGGTGTGATCTCATTATGTTACTCTGAAACGTATTGTGCAGCAGCACACTGGCGTTATAGAACTGCTTTCATTTAAATTCCATTAGGAATGTGTTTACACTGAAATATAAATGATATTTATCAAGTTGATAACTGTCATTTTTGATACATAATAATTTCTCTCTCTATATATATAAATAAAATGTATCTGTATATACATACAAAGAAACTATATATGTATATATATGTGTGTGTGTGTGTATATATATATATATATATGTATATATACATACATATATAAGGAATGTAGAGTGTACGTGACTGTGCGTACCACGTGATTTTTTTATTATTTTAG
Seq C2 exon
GGTAACGTAGGTCCCATTGGTCCTCCTGGTCCTGCTGGCCCACCTGGAGATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002552:ENSGALT00000004033:35
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(3.7=16.7),PF0139113=Collagen=FE(24.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(24.3=100),PF0139113=Collagen=PU(15.5=61.1)
Main Inclusion Isoform:
NA
Other Inclusion 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:
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]