BtaINT0118678 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038904 | PRRT1
Description
proline-rich transmembrane protein 1 [Source:HGNC Symbol;Acc:HGNC:13943]
Coordinates
chr23:27038200-27039760:+
Coord C1 exon
chr23:27038200-27038316
Coord A exon
chr23:27038317-27039224
Coord C2 exon
chr23:27039225-27039760
Length
908 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAA
5' ss Score
6.68
3' ss Seq
CCTCTGCTTACCGCCCCCAGGTC
3' ss Score
9.37
Exon sequences
Seq C1 exon
GCCGGCTGCGCAATCTGCGCACCCAGACTCCGGTGCTAGCCAGGGACCCCGACTCCGGACTCCGGCTGCACGGATCTTGTCCCAGGGAGAGCGCAAGCATGTCATCCGAAAAGTCAG
Seq A exon
GTAGAAAACAACAACAAACCCCTCGCCCTCTCCACTGCCTCCAGACTACCCCCCCTCCCTTACCCCTCCCTAGCGGGTGGTTCTGTTTCATTCCCCTTCTATCCAGCTCTCCATATCCCTCCCCCCAAGCCCCCTTCTCTTTCTATATCCTTCCCTTTTCTTCCTTTCCTCTGGCCAGTCTCAGGCTCGGTCCCTTGCCAACAACACTGGGGGGGAGGGGGGCAGGTTAAGAGGGTGAGGGAAGTACAAGACTGGCTTAGCATCAGCCAGGTACTGCACGGATAGCATCATTGGGAGTGACAGATGGACAGATAACGCTGGCCCGCATGGAGACATCCAGCGGGGTAATATGGAGAGATGATCAGATGGGGATTGCCAGGGGAGTAAAATCCAGAGGACCCTTCTTAATCTGCCCTAAAAGAGGTTCGGAGATTCCAAGAGAGACTAGGGGACCCCCTCCCCACTAAAGGAATGGCAGAGTGGAACATGTTATCCTACATGTGTTTATACAACTGTTGGACTGAGCACATGTTCACACAAGTGTTGCATGTCTATACATGTGCACACGCAGGACTAGCTCAGATAGGCAAACCCCAAAGCAGCCATAAGCCAAGAGGGTTAGGAGTTTGGGTCTGCAGGTTAAAGCTGTGTGCCCACTGCTGAAGCAGGGAGAGGAGCAGAAGAGAGTTATGACCTCAAAACTAGATTAAAGTGGGGGCGGGGGGAAAGGGCTGTTGGCCTAGATACCACCCCTCTCCTCCCCCAAGAATGAGAGATGGCTTCTCACTCATCTCCTCTCTGTCTCTCCCATTATCTTTCTCCGTCCCTGACCCTCTGTGTCTCCCCCTCTCCCTCATCTCATCTATCTTATCTCTCCCCATACTGGCTCCTCTGCTTACCGCCCCCAG
Seq C2 exon
GTCTCCCTGACTCAGTCCCTCACACCTCTCCACCACCCTACAATGCCCCCCAGCCCCCCGCCGAACCTCCTGCCCCGCCCCCACAGACAGCCCCTTCCTCGCACCATCACCACCACCACCACTACCACCAGTCCGGCACTGCCACCCTCCCGCGCTTAGGGGCAGGGGGCCTGGCTTCTGGGGCCGCCGCTCAGCGCGGTCCCTCGTCCTCCGCTACCTTGCCAAGGCCCCCACACCATGCCCCTCCTGGCCCGGCCGCTGGGGCGCCCCCACCCGGCTGCGCTACCTTGCCCCGCATGCCACCCGACCCTTACCTGCAGGAGACTCGCTTCGAGGGCCCACTGCCCCCACCGCCGCCCGCCGCCGCCGCCCCGCCCCCGCCGGCGACCTCTCATACTGCCCAGGCCCCGGGCTTCGTGGTGCCCACGCACACGGGAGCGGTAGGCACGCTGCCGCTGGGTGGCTACGTAGCCCCGGGTTACCCTTTACAGCTGCAGCCTTGCACTGCCTACGTGCCGGTCTACCCGGTGGGCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038904:ENSBTAT00000010290:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.816
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCAAGCATGTCATCCGAAAA
R:
AGTCTCCTGCAGGTAAGGGTC
Band lengths:
352-1260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]