BtaINT0107385 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011680 | PAPLN
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:HGNC Symbol;Acc:HGNC:19262]
Coordinates
chr10:85101226-85102283:+
Coord C1 exon
chr10:85101226-85101359
Coord A exon
chr10:85101360-85102159
Coord C2 exon
chr10:85102160-85102283
Length
800 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CTCTCACCTCCGCCTGGCAGGTC
3' ss Score
9.94
Exon sequences
Seq C1 exon
CAGCCCCCAACAAATGTGAGCTGAACTGCATCCCCAAGGGGGAGAGCTTTTACTACAAGCACAAGGAGGCCGTTGTAGACGGGACACCCTGTGAACCTGGCAGACGGGACATCTGTGTGGATGGCAGCTGCAGG
Seq A exon
GTGAGTTGTCCCCGCCACCCCCACCAGCAGGTTTGGGGCTCATTACAGGATGTCCACCTGCCCCCCCACCAGAGGCTCTCCTGACCATGATGCCTTCTCAAGACTAGCTTCTAAGGTGCCTTGCATCTCCGATGTCCTGTGGCCCTCTTACCTTTGCCCTTTGAAAACTCAACAATAAGAGGAAGCTTCTGGGTGGCAAGTTAGTAAAAGTAAAAGTGACTTAAGGGGGAAAAAAAGCCATTGAGGGAGGGGCTGGCTGGCTGCAGGGGCCTGGCTGATGCTCTGGAAAATCTCTCCTCGCTTGGCTTTCTTCTCCTCTGGGTCCGCTGAGGGTTGGCGAGTTCTTCTGGTGAGCTGTGAAGATGGCCCAGTGGCCCCAGGCTTCTGTTGTCATAGCCTGGCCGCTCCCTGGGGCAGGGGCGCTGTTCCCAGAAGTGCCAGCAACGCGGGGTTGCCTCTGGCTTGCCCTCACCTGGGGCTCCCCCGAACGCCTTGAGCAAAGCGCACAGCCTGCTGACCAGCCCGACACTACTGCCCGGAAGCCATGTCCACACGCTGTGGGAGAGAGGTGGCTTCCGAAGGAAAACGAGGTGCTGTTGCCGGAGAAGGGGACGCGGGCGCCGTGCAGGCAGGAGAGGTGGATGATCAGCTACCGGCCAGGTTCAAGGCTAACTCGGCGCCCCTGGCCAGCGAATGGTTACCGCACCTCCTGGGACTGGCCGGGCGGCCAGGGTTCCAGTCCGGGTGTGACCGTGACCCCCCCTGGGTCTCTCGCATCTCCTCTCACCTCCGCCTGGCAG
Seq C2 exon
GTCGTTGGCTGTGACCACCACCTGGACTCGTCGAAGGAGGAGGACAAGTGTCTGCGGTGCGGGGGTGACGGCACGACCTGCTACCCTGTCACGGGCGTCTTTGAGGCCAATGACCTCAGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011680:ENSBTAT00000015505:4
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF059869=ADAM_spacer1=PU(11.9=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCCAACAAATGTGAGCTGA
R:
TCTGCTGAGGTCATTGGCCTC
Band lengths:
254-1054
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development