BtaINT0042229 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012837 | COL6A6
Description
collagen, type VI, alpha 6 [Source:HGNC Symbol;Acc:HGNC:27023]
Coordinates
chr1:153435372-153438339:-
Coord C1 exon
chr1:153438273-153438339
Coord A exon
chr1:153435960-153438272
Coord C2 exon
chr1:153435372-153435959
Length
2313 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
GTTTGTCTGTGGGTTTGTAGGCC
3' ss Score
7.77
Exon sequences
Seq C1 exon
ATGAAAATGCTGCTCATTTTGTTCCTTATAATAATTTGTTCCCATGTTTCTGTCAACCAACATTCTG
Seq A exon
GTAAGGAAAATAATGAAAGGAATTCATTTCCTTAATTCTCATTATGGAAAATAGATAATATATGAGTCTGACTTGCTTAAAATTTAAGAGTTTTGTTTTGTTTTGTTTTGACTGTGATGATGGGGGTGGGGTGGGGAGTGAAAGCTCAATTTCTTTGATGTCACCCCATGTTCCTTTGAAAACCATTTGTTTCTGGGGTTTATTCCCTTTTCATGATAGAAAGATATGAGAGCTGTTTTCTTGTCCTCCAGTTTCAACTTCTTCTAGGTCTTCTGGGAGGTTGCGTTTTCATGCAACCTTCTCTTTTCACATTAAGTTTGGGCCTGGAAAATTTGAAATGTCTGTTCCTAGTTTGTTTGTTCCAAAATATCTGTCTTGGTCAAACATCCAGATTTGGCTCCAGTTGAAACTGTGTGTCTGCTTATTGTAAAGCAGGTGCTTTTTACCCTGAAGAGGGAACTCCAGAGCTGTCCACTGTCTGTCAGCAGTCTATGTCCAAATGGACTTGAAGTCAAAATACTGGTCAAGCCTTCACGGCCCTTACCGTCTCCTAAATAACCAGTCACTTCATGTCCAGGGCCACCTAGATTGGTTTTACAGTTTTGTTTTTTTTTTTTTTCAAGGACTCTGACCTTGGAAGCAACTTTTCTGGAGAGATAAATTCTTCTTTGCCCTGAAAACATATTCCTTTGATGTCTCACTGGGCCTGATATTAAGCTTTTCAAAGAGAGGCGATGCTTTTTCTCCAGTTGCTCCATGGTTCAGATACAGTGATGGGCCCGTCCTGTGCCAGTGGCTACATTTCTTTTCTCCACCAGGATGTGGGGGTTTGTCTGTGAATAGAAAGCTCACTTTTGGTCCCAAGTTGAGCCACCCTGGGCAGTCCTCACCTGACAGCTCTCGGAGGGGCCCCAGCCTTCTCTCGCTGGTTCCCCTCACTTAGTATTTTCCCAGAGATGCTGCTGGATATAGGATCATCAGAGTCTCAGACTGGCTGAAATCAGGTTGCTTAGAAGAAAAGAAAGGACAATTGGAATCCACTATGCCTTGATTGGACTACTCTAAAGAGAATAAAGTAACATGCAGGGGTACTAAGGCTGTTTTCCTAGCAGTTGTTGACAGGAAAAAACTGAAGTTCCTTTAATTTTATCAGAATTTATATAGTAACTATTTCAAATAATCAGAATATCAGAGTAAAGAGAGACCTTAGATATTTTCTAGTCGAATCTACCCATTTTAATTATGAGGAAACTGAGGCCCAAGTATGTCAGATGGCTTGACAGAGCTGGGAGAATTAGCTGATAACAAAGTTAAGACTCGCATTGCCTGTTCAGTTACACTGTGTTTTCTTAAACATACAACATCAAGACACACACAGGTATGTCCCTCCCTTCCCTGGACAAGACATGGATCTTATAGGACAGTCATGAGAGCTCTGAATTCAAGCCAGCAGACAAACCACCAGCATATTATATTTTGTGCTTGAACCAAATGCTTCTCTATCACATACAAATATAATTTCACATACCTAACATTCAATCTGGCATTGAATGAAGCCTTAAAATCTCAGCAAAGTATTGCATTCCTATGTAAAAATTACATTATCAATAGAAACTTAAACTGTAATCTCTTTCCTAGCTTAAGGTATACTGGTTTCTGTCACATTTTTCATATGTAAGAATAAATTTACCAATTATAATGCCCACTCATGACTCGTCAAAAGATATCATAAATAATTTTAAGATAGATTAATACATCTCATATTTATGATTTTTAGGATTTTGTAAAACTCATCAATTTGACACTTCGAATACAAAACTAACATGTTTATAAGTTTAATATGTTTATAAGTTAATTAGGTTACTTGTACTGTTTAAAAGGAAGTCAAAATGAAAGGCTATTTTTCAGATTTCTCCATTCAACAAATTTGATTCATTCTCAATGAAACTGTTTATCTTGTTTCTATAAACTGAGGTCAAATTCTGAAAGAAGAAAAGGATACAAAGGGAAATTATCCACTAACCATGTAAAAACCCATGATATTTTACTTCTTTATATGTAGCTATTTCTATTTAATTCCTTGCAAAAGTGGTACTTACTTTCATGATCAGTTCAAATGAGAAGGTGTATAAAAGAATTAGCCTGAGAAACAAATACTTTCATTGAGAGAATATGTATTATTTTTCAGTGCATTGGAAAGATGTTACAAAGGCAAGTAAAAGAGGGAAGTCAGTTTTCCCCATGTGGTTGGCATTAAGCTTGGTAGTAAATGTTTGAAGTTTACTTTCACTGTGTTTGTCTGTGGGTTTGTAG
Seq C2 exon
GCCCTGAGTATGCTGATGTGGTGTTTCTGGTGGACAGCTCCGACCACCTGGGAATTAAGTCCTTCCCATTTGTGAAGGCCTTCATCAACAAGATGATCAGCAGCCTCCCCATAGAGGCTGACAAGTACCACGTGGGCCTGGCCCAGTACAGCGATGGGCTCCACAGAGAGTTCCTGCTCAGCACCTTCAAGAGCAGGGGCCCCATGCTGAACCACCTCAAGAAGAACTTCGGGTTCCTGGGGGGCTCCCTGCAGGTTGGGAAGGCTCTCCGGGAGGTGCACAGGGCCTACTTCTCAAGCGGGAGGGACAGGAAACAGTTTCCCCCGATCCTGGTGGTCCTGGCCTCCGGCGAGTCTGAAGATGCTGTGGAAGAGGCCGCCGAAGCGCTGCGCAAAGATGGGGTGAGGATCGTCTCCGTGGGGATGCAGGGCGTGTCCGAGAAGACCCTGAAGGCCATGGCCACGGGCCAGTTCCACTACAACCTCCGGACTGTCAGGGACCTCAGCTCGTTCTCCCAAAACATGACGCAGATTCTCAAGGATGCAGCTCAGTACAAGGACAGGGCAGTCAATGACATCCTTGTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012837:ENSBTAT00000017057:1
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=WD(100=88.3)
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:
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]
SPECIAL DATASETS
- Pre-implantation embryo development