DreINT0049442 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41405562-41406601:+
Coord C1 exon
chr19:41405562-41405615
Coord A exon
chr19:41405616-41406502
Coord C2 exon
chr19:41406503-41406601
Length
887 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
CTATGAATGCTGTACCTCAGGGC
3' ss Score
5.38
Exon sequences
Seq C1 exon
GGAGCCGCTGGTACTCGTGGTCTGCCTGGTCTGGCTGGCAGGTCAGGCCCAATG
Seq A exon
GTAAGATTTAAGAAATATTACCCATTTTGCACTATATCTTATATTATGCTATTTTAGTTTATATGCATATACAGTAGAGGCCAAAAAATGTTGTCTACAGAGGACATTTGCACAATATTTGCTTTTATTTATCAAAATATTGGAATAATTTTATATTGGGTTAGGGACAACGCCAAATTTGTTTAGCACGTGGGTAGCACGTTCGCCTCACAGCAAGAACGTCGCTGGGTCGCTGGTTCGAGCCTCGGCTCAGTTGGCGTTTCTGTGTGGAGTTTGCATGTTCTCCCTGCATTCGTGTGGGTTTCCTCCGGGTGCTCCGGTTTCCCCCACAGTCCAAAGACATGCGGTACAGGTGAATTGGGTAGGCTAAATTGTCCGTATTGTGTGTGTGTGTGAATGACTGTGTGTGGATGTTTCCCAGAGATGGGTTGCGGCTGGAAGGGCATCCGCTGTGTAAAAACTTGCTGGATAAGTTGGCAGTTCATTCCGCTGTGGCGACCCCGGATTAATAAATGGACTAAGCTGACAAAAAAATGAGTGAAAAATTGGCTAAGCTACAGCTTATAATGGAATGTTTGTATTATTAAGCAATGCAAAGAAACTCAATGTGTAAATAAAATGTACATTCACTACAGATTAATCATTTATTAATATTTAATTGGTTCAATTTTGTATTTAAATAAAATCAATTCCCCTGCGATTTCTCAATAAACTTCCATCATTGGGTTATTTCCAATGAAACAATTGAAATATGTAGCACATACAAACGGGACATCACTATTGGCCACAACTGTATTTAATCATTCACCTGCTAATCACTGTAATTCCATGCAGATTTACATTGATCTGAAGCTGTAAGACTCTAATCTATGAATGCTGTACCTCAG
Seq C2 exon
GGCATGCCTGGTCCTCGTGGTGGTGTTGGTGCACCTGGAGCCCGTGGACCTCCTGGAGATGCTGGTCGTGCTGGTGAGGCTGGTCTTGTTGGAGCCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:20
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=FE(26.6=100),PF0139113=Collagen=PU(13.2=50.0)
A:
NA
C2:
PF0139113=Collagen=PD(4.7=9.1),PF0139113=Collagen=FE(47.1=100),PF0139113=Collagen=PU(2.3=6.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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]