DreINT0049382 @ danRer10
Intron Retention
Gene
ENSDARG00000035809 | col1a1b
Description
collagen, type I, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-030131-4400]
Coordinates
chr12:3097293-3098750:-
Coord C1 exon
chr12:3098548-3098750
Coord A exon
chr12:3097482-3098547
Coord C2 exon
chr12:3097293-3097481
Length
1066 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
CATGCTTCTTGTCCTTGCAGTCT
3' ss Score
10.64
Exon sequences
Seq C1 exon
GCAGTAGGGAGTTTCTGCTAGGGTCTGGATTGGAGTTACACAGACCGGACCCTACGTGTATGAGTGAGGACAAAACAGGATTCCCCTAGCCTCAAAGAGTCTACATGTCTAATATTTAGACATGTTCAGCTTTGTGGATATCCGGTTAGGGCTGCTGCTCGCCGCAGTGGTCCTTGCAGTGAGAGGACAAGGAGAGGATGACA
Seq A exon
GTGAGTATGATTTTTACTCCTGCTTTTAACTCCAAAGATGCTTGACAGTGGACACTGGAGAACTGAGGAGGGGGAGATGTTGCAGCTCACCTGCACTCTGAAACTTTCTTGGGAATGTCTTGAGGAGGAAAGCCCTACCTTTTTATTCTCACCAGCGTTTTTTTAAAACTTCTAGAAATCTTTCTTTGTGCATCTTGCGGAGTTGTTGTTTCTTCATCGTGCTTGTTTCCTGCGCGCGTGCCCTTACATGTTAAGCGCGAGCACGCGCGCCTGAGTGATGTCCTCGAGCGAAGGATGCGCTGAAGGAAAAGACGACGAAAAGAAGAGAAGAGGGCTTTTAAAATCACTTATCTTCTCATTTTCACGCTTCTCAGTATTCTGTCATACATTTATCATTCGAAAACAGGATATAAACCCGCTTATCTGTGGATTACACTGCTTTTGTGATAGAACAGATGCAGCCGTTACTCTTGTAAACAAACGGTTTTGTCAGGGTTAGCTTAGCCGTTAAGGTTTAACAATATACTTACAATTTCGCGTTTCTAAATGACAAACAAGATTTTTATTTGATATGGAAAACCCTTTAGTTTCCAGTTCATTAATTGTGAGTGTTCGGGGCGTGACGGTGCATTGAACAGTCAATAGCGCCACCAAGCGGTGGATTTTAACACTATATAGTCTTAAACATGATGAAGGCCTGTCTTTAACATCATCACCCTAATGCACCACGCCCAATTACACTATTTTATCCTAATTTTAAAGATTTTTAACAGTTAAATTAAAACAGTAAGGTCTCTAATGTTCACTCTCTGCATTTTGCAAGAGTAATGCCATTATCGTTGCTTTTGTGTTATACTTACCATATATTTCCTTCTAAATGTAACCTAGAGGTGTTTGTATTTGTATGTTTTAGAGACTTTTTTATTCACTTAGCACTCTGAGGGTGATATTTAGTTGCCTGTTTGGTTACAATTATCTTTTAAAATCAAATTGGGATATTATTGTGGACCCTTCAGTTCAATTGATTATCCTCCACTGTCCTAATTCATGCTTCTTGTCCTTGCAG
Seq C2 exon
TCTCATTCGGTAGCTGTACATTGGAGGGTCAGAATTACAACGACAAGGATGTATGGAAACCCGAGCCCTGCCAAATCTGCGTCTGCGACAGCGGGACGGTCATGTGCGACGAGGTGATCTGCGAGGATACATCAGACTGTGCCAATCCAGAGATTCCCGATGGAGAATGCTGCCCCATCTGCCCCGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035809:ENSDART00000015092:1
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=0.062
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009313=VWC=WD(100=87.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGACCGGACCCTACGTGTAT
R:
GATGGGGCAGCATTCTCCATC
Band lengths:
342-1408
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]