BtaINT0042192 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030190 | COL6A3
Description
collagen, type VI, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2213]
Coordinates
chr3:117449473-117451031:-
Coord C1 exon
chr3:117450886-117451031
Coord A exon
chr3:117449566-117450885
Coord C2 exon
chr3:117449473-117449565
Length
1320 bp
Sequences
Splice sites
5' ss Seq
CTTGTGAGT
5' ss Score
7.15
3' ss Seq
TTTGCCTTTTGTCTCGGTAGGAC
3' ss Score
10.11
Exon sequences
Seq C1 exon
GTGTCCGAGCTCTGATCTTGGTGGGCCTCGAACGCGTCGCCAACTTGGAGCAGCTCATGCAGCTGGAGTTCGGGCGAGGGTTCACGTACAACCGGCCCCTGAGGCTGAACTTGCTGGACCTGGACTACGAACTAGCCGAGCAGCTT
Seq A exon
GTGAGTGTTTTGTGTGTCTACATGTTGGTCTAGATGCCGCAGGTTGGGGCATCCCAGGATAATACAGTCCGTTATCACCAGGCAAATGGAGGAGAGACTCCTGGGTGGGCAGTTTAACTCATCTGATTCACTAGGGACCTGCTTTGTTGCCACCACACGAGTCCTCGGAAGGGAGCTCTCTGAGGACTGGAAAGACGGCCACCTGGGAGACGGGTGTCCAGGCAGCGTTGCCTCAGAGTGGCCTCTACGTCGTGAACGAGGCGTTTTCCCCTTTATAAGACGGCTGAGAAGATATAACATTGAGATCGACCCGCTCCAAGCCAAAAACAGGGAAGACAAGAGTAGGCAGGAAAGAGAGATCATCTCTGGGTGGAAAGGGGCTTCTGTCGCCTTCTCTTCTAGTTTTCTTTGCTGCAAATGAGGACAGACCATGAGGCTTCCTAATCCCCCTGAGTTCAACCTCTCAGCTGGTGGGTTTAACTCCTGGGCTAGGGGTGAGCCTGGGGGTTTTGGGGTGTGGGCCTGAGTGTTCAACTCAGAGACTCTTTGGCGGAGGCAGCAGTGAACTGCAGAATTCAGTGACTCTGCCCATTCTTTCCTTCCTGCCTTCTTCCTAGGACCGGAGTTAGGATTTTTTTTTTTTTTTTGAGTGGAAGGAGGTTAGTGGACAAATTTTGGACTTGGGAGAGCGTGAAAATTCTAGGAAATTCACTACAAGCAAATGCATTGACCCTCATGAGTTCAGCAGGTGGAAATATGTCCTGGGTGTGCGCTTTCCCACATGAGGCCAGGGGCTGGGCTGGGAGGTCGTGTCCAGGGTGTCTGATGGATGTTGGAGGCCTTGGTGACCAGAGGTTGGGGTGCTCATGGCTCAGGCAGGGACCCCACCCCATGGCCACTCCTAGGCCTTCTCTCAAGGCAGGTACCCTGTTCTGTGACTCTGCCCAGGGCTCAGGGAAAGACATTTGGTCTGCTCTAAAACCCTCTTCCATCCTGGACGTCTGCAAGGGTTTGTTAGGCTTTGCTTTTTGCAGCTTAAAAATGTCTATGTTATACTTAGCAACTGAAGCTTGACTATCTATGCTGGAAACTTTAGAAGTAAGGCCCAGCCTTAGGTGAATATTTTATGAATAGGATGTATTATCTTTGGTGGCTCTTCAGACTCTGTTTGTGACATCCCATAGCATGCTGAAGGCTAAGTCTTCGAGGAAATGCCACTGGGAGTGATGTCATTTCTTGCTGTGAATGCCACATTCCTCAGACTTACGATTTTTTCCTAGGCAGTTACTGAGGGGTGAACTTTGCCTTTTGTCTCGGTAG
Seq C2 exon
GACAACATTGCTGAGAAAGCCTGCTGTGGGATTCCCTGCAAATGCTCTGGACAAAGAGGAGACCGAGGGCCCATAGGCAGCATCGGGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030190:ENSBTAT00000018479:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.355
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(25.8=51.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTCCGAGCTCTGATCTTGG
R:
TTTGGCCCGATGCTGCCTAT
Band lengths:
238-1558
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]