DreINT0050224 @ danRer10
Intron Retention
Gene
ENSDARG00000077139 | col6a3
Description
collagen, type VI, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-070501-8]
Coordinates
chr9:24129539-24131040:-
Coord C1 exon
chr9:24130441-24131040
Coord A exon
chr9:24130139-24130440
Coord C2 exon
chr9:24129539-24130138
Length
302 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
CATGAATCTTTGTTTCTAAGCTG
3' ss Score
4.16
Exon sequences
Seq C1 exon
CTGAGCCCAGGATGGCTAGGAGGGATGTAGTGTTTCTGCTGGATGGTTCAGATGGCACGAGGAGCTCTTTCTCTGCAATGCGAGACTTTGTTGAAAGGATGGTGGAAAGACTGAACGTGTCTGAGAACAGAGACCGTGTCTCTGTGGTCCAGTACAGCAGAGATCCAGAGGCTCATTTCTATCTGAACACATACTCAAGAAAAGAGGACGCTCTTGACACGATCAGGGGTCTGAGGCACAAAGGAGGGAGACCCCTCAACACGGGGGCAGCTCTGCAGTACTTGAGAGACAATGTCTTCACTGCCTCCTCTGGAAGTAGACGTGTAGAAGGTGTTCCTCAGTTGCTGATTCTGCTGAGTGGCGCAAGGTCATTTGATAATGTTGACACGCCAGCCTCATCCCTAAAGGAGCTGGGAGTGCTTATCTTTGCGATTGGGTCAAGGAGCTCAGACAGCCAGGAACTCCAGAGAATCTCCCAAGAGCCTAGCTATGCACTCTCAGTGAGTGACTTCACTGACCTTCCCAGTGTCCAACAGCAGCTTTTTACCAACATTAACAAGGTCTTTGTAGCGGGCGTACCTACCACTTCCACAACCATAG
Seq A exon
GTAAGAAAAAGCCAAAGTGGCTTCCAGTAGTTTCCAATCACTTTTTATTAGTCGCAACGACATGTGCTTTGCTGTTCCCGTATCGCTAATGAGTTGTTGAACAGGTCAAAATTTTGTGACCCCTAAAACGCAATGAGAGGTGATGTGATAGGCAAAAGAAGAAGAAGAAAAAAAAGCATGATCAGTGACAAAGCACCAAGACTGCAACTTATTATTATATTAATATGATTATTGTTCTTATTTATTGATATTGCATCTCCTTAAAATAGTTCCCATCTGACTCATGAATCTTTGTTTCTAAG
Seq C2 exon
CTGAGGGCCGTAGACAGAGAAGAGATGTTGTGTTCCTTCTGGATGGATCGGATGGAACTAGGAATGGATTCCCAGCAATGAAAGACTTTGTGCAAAGAATGGTGGAGAAATTGGATGTTGCCGAGAACAGAGATCGCATTTCTGTTGTCCAATACAGCAGAGAACCAGGGGCCAATTTCTATCTAAACACATACACGACAAAGGAAGAAATTGTTGATGCTGTCAGGGGTCTGAGGCACAAGGGAGGCAGACCCCTTTACACGGGGGAAGCTCTCCAGTACGTCAGAGACAATGTCTTCACTGCTTCTTCTGGCAGCAGGCGGCTGGAGGGTGTGCCGCAGATACTGGTTTTGCTTAGCGGGGGCAGGTCATTTGACAGTGTCAATGCAGCAGCCTCCTCTCTGAAAGAGCTTGGCGTCTTGACTTTTGGAATAGGATCGAGAGGCTCTGATAGCAGAGAACTGCAGAGAATATCATATGAACCCAGTTATGCTCTGTCCGTGTCTGATTTCAGTGAGCTACCAAATGTCCAAGAGCAGCTGCTTGCCTCTGTACAGGTTACTTCAATTCCCGTCACCCCAACTTCACCGACTGTTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077139:ENSDART00000138754:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.075 A=NA C2=0.030
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=88.5)
A:
NA
C2:
PF0009223=VWA=WD(100=86.5),PF119183=DUF3436=WD(100=26.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTTTGTAGCGGGCGTACCTA
R:
GCTGCCAGAAGAAGCAGTGAA
Band lengths:
356-658
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]