BtaINT0107375 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011680 | PAPLN
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:HGNC Symbol;Acc:HGNC:19262]
Coordinates
chr10:85115314-85116890:+
Coord C1 exon
chr10:85115314-85115452
Coord A exon
chr10:85115453-85116427
Coord C2 exon
chr10:85116428-85116890
Length
975 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
GTGCTTCCTGCCCCCCTCAGCGT
3' ss Score
8.53
Exon sequences
Seq C1 exon
GTCCCCAATGCCCACCGGCCCCAGGCCCAGCAGAATGAGCCCAGCGAGTGCCGGGGCTCCCAGTTCGGCTGCTGCTATGACCACGTGGCCCCTGCGGCAGGTCCTCTGGGGGAAGGCTGTGTGGGCCAGCCCAGCTCTG
Seq A exon
GTGAGTGGCTGATCCTCCTCGTCCTTATTGGTGGGAAGGCTCTCGTCCCACTCTGCTCACTGCCCCGCCCCCCCAGAGCCCCCCGACTTCCTCCTGGCTGGCTTACCACTTGTTTCTCCCACCAATATTCCTGGCACCTGCCAGGTCCTGGGCTGGAGAACGGTGCTGGATTATTCTGCCCGACAGGTCATCCTCGCCCCTGAGTTTGCACTCGTGGCCGCCTGGCTGCCTGTGGGAGCCGGGAGCGTGGTCAGTGGGGAGTCCATGGAGAAGGAAGACCTGTGCTACCCCTTGGGGCTCAGCCCCCTCCAGAGGCAGTGGGGGGGTGGTCAAGACTGGGATGGATGGGGTGGCCACCCTGCCTGAGATGCGTCTTGGAGGAAGGACCATGAGGTGGGAGCACATGCCCACGTGGAGCTGCTAAGGACCATCCCGGGGATGCCGGAAGCCAGGGGGCAGAGTCTGCAGGGAGCTGGGTGGGGGGGCTTGAAGTGGGGGGTCTGGAGGGTCACATCTGAGTGTGGAGAAGGATGGCTAGGCTGGGGGCTGGAGAAGGTTCTGAGCTGCTAAGGGGCCCCAGGAACAAGGGTGGACCCCCTCCCTGGGCATCTTGGCAGCCTGTGGGGGCTCAGGGCTGGGGGTATTCCTTCTGCGCGAAGCACGTCAAAGGTTGGCCCTGGGGCTGCTCTGTGTGCGCTGGGGGCCTGGGTCGGGTGGGGAGGAGCACGAGGGAGCCCGTCCAGGGAGGTCACAGCCCTGATCCTCTGCAGGGCTCCAGCTCTGGGGGTGCAGAACAGGCTGGTTCTGCTGGGGTCCCGGGGCAGTGAGCAGAGTCTGTCCCTGGAGTCAGTCAAGCTCCCGGCAGTAGTGTGGATGTGCGCTGAAGCTGGGGAGGGCCTCGCTCCTGAGTCCCGGGCTGCGTTCGCAGCTTCCCTACTGAGTCCCGGTGACCTGCGTGCTTCCTGCCCCCCTCAG
Seq C2 exon
CGTACCCCGTGCGGTGCCTGCTGCCCAGCGCCCACGGCTCCTGCACCGACTGGGCTGCCCGCTGGTACTTCGTCCCCTCCGTGGGCCAGTGTAACCGCTTCTGGTATGGCGGCTGCCATGGCAACGCCAACAACTTTGCCTCGGAAGAGGAGTGTGTGAGTGCCTGCCGGGGACCCCAGCCCGGGGCGGGGGCCTCTGGCCAGAGCACCCATGGAGATGGTGGCAGCAGCGGTCCTGGGGGCCAGCAGGAGGCTAGCCAGCATGGGCCGGGGCCCATGGTCCAGAGAGGACCCTTGCCTTCCGGTGGCCTCCGGTGGCAAGACCAAGAGCCTGGGCCGGGGGTGACGGACCACAGACAGGCCTTTGGAGAGGGGCCCTGGGGCCAGGAGACTGGGCCCAGTCCCCCTGGACTGAGCGGAGACGCAGGACGACCAGCGCCTCCTTCCCGTGGCTCCTCCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011680:ENSBTAT00000015505:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.298 A=NA C2=0.658
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0001418=Kunitz_BPTI=WD(100=34.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGTCCTCTGGGGGAAGG
R:
GGAAGGCAAGGGTCCTCTCT
Band lengths:
344-1319
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development