BtaINT0117271 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002158 | PRDM9
Description
PR domain containing 9 [Source:HGNC Symbol;Acc:HGNC:13994]
Coordinates
chrX:143416113-143418429:-
Coord C1 exon
chrX:143418236-143418429
Coord A exon
chrX:143416555-143418235
Coord C2 exon
chrX:143416113-143416554
Length
1681 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTAAAAGCTTCTTCTTTCAGCAG
3' ss Score
4.44
Exon sequences
Seq C1 exon
GTATGTGAACTGTGCCCGGGATGATGAGGAGCAGAACCTGGTGGCCTTGCAGTATCACGGGCAGATCTTCTACCGAACCTGCCGGGTGGTCAGGCCGGGCTGTGAGCTGCTGGTCTGGTATGGGGACGAGTATGGCGAGGAACTCGGCATCAAGCAGGACAAAAGGGGGAAGAGCAAGCTCTCGGCCCAGAGAG
Seq A exon
GTGAGCGCCAGCCCTCTTCCAGCACTCCACCCCATCCTGGGGAGCTTCCCTGGTCCTATTCTGAAGCACAGTCCAATCCAGTCTAAAGTCAGTCAAGTTGCAATTAAAATGCCTCAGAATTTGATTCATTTCATAAGACTGTTAGGAAAAATATTTATATTAAAAATATTAGTTCTAATTTTCAATATTTCATGCAAAAAATATGTAACATCACCTTCTTCTGAAAGGCTTAGAAGCAAAAAGCAAGTTTTTTAGCACCTACCAGCTCTCTCACCTTTACCAGTTTCTTCCTCATTTCCTCCACATTTCTAAGTGACATGCATACAGTGATTTGCATTCAGTTACTGTTTCAGTTTGTTGTCATGTGAATTCATACTTTGTGCCAGACAGGGCTACACACACTGAAGCAGACAGAACCACTGCCTTGGGGCAGCGTGGGCTTCATACCAGACAGGGGCTGGTGCTCTGAGGAAAACCAGTGCAGTAAAGTGCCTCGGATCAGCATGCACAGAGTGGGGTGTGGCAGAGGATGGTGGGGCAGGGTCTCTGCAGAGATAACACCTGTGGATTCCAGGATTCCAGGCAGGGGAGCAGCCAGTGCTGCAGCCTCAGGGCCGGGAAGAGAGGCCATGTCAGTGGTCGCAGGAGGAAGCACAGAGGGAGAGGAAGGAGGCTGGATGGAACACAGAAGCCTCAGCGCCCATGTCCATGTGCAGGCCTTAGGGGTCTTCCTGGGTGACACAGAACAACCATGTGGCTATCAGCTCCAAGCGGCATGTTCTCTGTGCTAAGATGATGCTTTGGTTCATTTTTGGGAAGAGACAGCAGTGGGGAGTCCCCTCAGAGGTCAGTTCATTGCCAGACATGAGGGGAGAGTGGCCTGGGTAAAGATGCTTGGGAGTGAGGGTGTGAAGAGTCTGGCTGGAGATGTATTTTTAAGCAGGACTTCCTAGTGCATGTTAAATGGACTAAGACTGTGTGAAATAAGAGGTATGAGTATTGATGAGGCTTGAGAAAGGACATGTCTTTATTGTATGATGTATAGAAAACAGAGAGGAGCAATTTATGAACCAACCAGGGCAGCAGGAGCCAGAGACCTGTAGTCAGTAGGACCTGGGCCTCTTGGTCTCGTCCAGTCTCAAACCCACTTCCTGCAGAGTGGTTTCTTTGAAAGGCTGCTCTTTGAACAAGAAGCCTCAAATTCAGCTTTACTCACACCTGCTCTAACCACCCCCTGTGCTGCCTCCCATATGCAGAGAGCTCCAGGCCAGGTGCCCCTAACTTAATAGACCCTTTCCCCTCACAGGGAGCCATTCAGGAAGATTCCACCTAAGTCATCAAGAGTCTTATCTCTCAGTAGGGTAAAATACCTGTGGCCACTGTGACACGACTTTTCAGATACTTACACTCAGGGAAAGGTCCCTGCAGATCCACCTCTATCAGGAGAGACGCTGCCTCTGATGCTACTGAAAGGTCCCTAGGCTGGGTGGTATGTAGAAAAGGCCCTTGATGCAAGCTTCCTGGATTTCTGTAGATGTAGAGAATAAGAATGGAATGGATAAGTGGACTGTAAAGACCCACTTGATGGGAGACAAATCGTGCACCGTCAACACTAAGATGGTTACTGGGGCAGGCTTTACCATGGCACACCAGCTACCTGACTAAAAGCTTCTTCTTTCAG
Seq C2 exon
CAGAACCAAAGCCCAAGATCTACCCATGTGCCTCCTGCTGTCTATCCTTCTCCAGTCAGAAATTCCTCAGCCAACATGTCCAACGCAATCACCCTTCTCAGATCCTCCTGAGGCCATCTATAGGAGACCACCTCCAACCAGAGGATCCCTGTCCAGGCAGTCAAAATCAGCAGCAGCGATATTCTGATCCACACAGCCTGAGTGACAAACCAGAGGGTCGAGAGCCCAAGGAAAGGCCCCATCCTTTGCTGAAAGGCCCCAAACTTTGCATAAGGCCGAAGAGGATTTCAACGGCCTCTTCCTACCCACCCAAAGGACAAATGGGGGGTTCTGAGGTGCATGAGAGAATGACCGAAGAGCCCAGCACAAGCCAGAAACTGAATCCAGAGGACACAGGCAAATTATTCATGGAGGCAGGGGTCTCAGGGATTGTAAGAGTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002158:ENSBTAT00000056084:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.197 A=NA C2=0.723
Domain overlap (PFAM):
C1:
PF0085623=SET=PD(53.2=62.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGGGCAGATCTTCTACCGAA
R:
TCACTCAGGCTGTGTGGATCA
Band lengths:
343-2024
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]