BtaINT0065568 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006948 | GARNL3
Description
GTPase activating Rap/RanGAP domain-like 3 [Source:HGNC Symbol;Acc:HGNC:25425]
Coordinates
chr11:98154149-98155944:+
Coord C1 exon
chr11:98154149-98154364
Coord A exon
chr11:98154365-98155817
Coord C2 exon
chr11:98155818-98155944
Length
1453 bp
Sequences
Splice sites
5' ss Seq
TGGGTAATG
5' ss Score
5.68
3' ss Seq
GATTCTCCCCTCCCATCCAGGCC
3' ss Score
8.9
Exon sequences
Seq C1 exon
GTGAAATTCAGTCCAAAAATCTGTACAAGATTCCACTCAGAAACCTGGTGGGCAGAAGCATCGAGCGGCCTCTGAAATCGCCCTTAGTCTCCAAGGTCATCACCCCACCCACCTCCATCGGCATTGGCATCGCGGCCATTCCTGTCACTCACTCCTTGTCCCTGTCCCGCATGGAGATCAAAGAAATAGCAAGCAGGACCCGCAGGGAGCTGCTGG
Seq A exon
GTAATGGCTGTCCATTCTCGTGTTTGTGATGTTTGTAAAGATACCCGCTGATTTTATCTGCGCATATTGGTTGTGCTTAGTCATGTCTGACTTTTTGTGACTCCATGGACTGTAGCCCACCAGGCTCTTGTGTCCATGGAATTTTCCAGGTAAAAATACTGGAGCAGGCTGCCGTTTCCTCCCCCAGGGGACCATCCCAACCCAGGGGTTAAACCTGCGTCTCCTGCATTGGCAGGGGGGATTCTTTACCACTGTGCCTCTTGGGAAGACCATTTATGGATATTAATTATCCTCAAATGCAAAGAGCCCTATCATAAGGGATTTATAAAGAAATTATAAACTTGCACCCACACCAAGGAATACTGTACAGTCTGCCCAACAATGATGTGTCAATCTAGACTTATTGGTATAGAAAGTGTGCAAACCATATGAAGGGCAGGTGGGGAGGCAGTTTGTAAAACAGTCTGTCTAGTCTGATAACAGTTCTTTAAATATAAGTAATCTAAATAGGTATAATCCTAGAAAAGTGTCTAGAAGGGCTTACAGCCTGCAGCTCTCAGATAACATTTCATACTTATATATCCAAAATGTAAATCTGTCTGGGATTTTCTGCATATTTTTGTTCCCTTTTTTGCATATTTGTGGTGCAGTTCAGTCATCCCCTCTCGAAGCCCCTGGGCCAGGAGGCAGGTCTGTGGGGATGGGAGCAATGTCAGGTCCCTGCTATGCCCTCCTGTCAGTTCACAGGTGAGAGACCAGACCAGAGACATAAAGAGCACCATGATAATCGTGAAGAGGCTAGACTGTTGTAAAGGTTTTTGTTCAGAGTTGTGAAAACAAAATGAGGAAAAATGGAGGCATTATGGCAAAACAGTAAGAACTGGTTTAAAACTTGAATTGGCATCTGCATGGTGTAAAACTATGAGGACACACACCTGTCCTCTGGCCAAGTCTCCTGACCAGCTGGAGAAGGGGATTCAGATCCCCTGACAGGGCAACCTTGACACTGGCAAAATTGGTTGGCTCTTGAAGTTGGTCCCTTTCACTGAGCTTTTCAAATGTATGTATTGCTATTTTTAACCCATTATTCCCTAAGAAAGCTTGATCTTGCCAACTATTGTTGTATAAACCACTGTGCTTTTCAGAAATTGGACCTCTGAGTTGGCGAATTACAATTTCCAGTGGTAGGACTGTAGATTTTCTTTCCTTCATTAAACTCTTCTGAGTCATTTTTTCCCAATACATATATTCGTTCTAATCAGAAACAAAAGACCTTTTACCAACAAGACAATGAGAAAATCAATTATTTAAAAGTACAGACTTTTATCATCATTCTTCCTGCCTCCATCCCCGTAATGTACCAATACCCAACCAGGAGAAAAAGGGCATTTCCTGTCTCTTGGCAGTCTGATGGTAATGACCCTCTGACCTGTGATTCTCCCCTCCCATCCAG
Seq C2 exon
GCCTCTCTGATGACGGTGGATCCAGGTCAGAAGGAGCACCAAAGCCCAAGTCAAAGGCCCGGAAGCGGCTGGAAGAAAACCAAGGAGGCCCCAGGCCAGGGACGGTGCGGTCCACTAGCAGTGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006948:ENSBTAT00000009123:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.329 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAATTCAGTCCAAAAATCTGTACA
R:
CACTGCTAGTGGACCGCAC
Band lengths:
338-1791
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development