BtaINT0022811 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014312 | ATL1
Description
Bos taurus atlastin GTPase 1 (ATL1), mRNA. [Source:RefSeq mRNA;Acc:NM_001034631]
Coordinates
chr10:43561443-43563019:+
Coord C1 exon
chr10:43561443-43561514
Coord A exon
chr10:43561515-43562587
Coord C2 exon
chr10:43562588-43563019
Length
1073 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
ATACTTCCTATTTGATACAGATA
3' ss Score
5.91
Exon sequences
Seq C1 exon
GCCACAGCAGAAGCTAATAATTTAGCAGCCGTGGCAACTGCCAAGGATACATACAATAAAAAAATGGAAGAG
Seq A exon
GTAAGAATATTTTAAATCACGTTTTAAGTAAAATCAGTATTTCTTCCATGAACTCATTCTTCTTCCACGTTACACTGTATACACATGCAGAAGTGGCTCTGACTTACGCTTTCTCAGCCTATGTGTATCACATTTCTTTTTATTGTATTCCTCAAGTATTTTAAAAACAAATCAAGAGAACATGACATATGCAAAATTTAAATGTATTTTAAATGAATTCTCTCTATAACATATTTCTTTTTAAAGGGGTGGAGGAATACAGATTTTTCCAGTATTTATAAGATCTAAAGTAGCTAAAATAACATGCTACCCTCTCCACTATACCTCCCCGTATTCCACAAGTCCAATTTCTATCTTAAGTATAAAAACTTGTTAGAAACAAATAAACCACAAGGGCCAACATTTCTAAGTACTATATTTCCTCTTTTTACTAGTAACATTCTAAATTAGGATGCATCTACTGATTATTGTGTATATCTATTAATGTGATGAGTTTTCTTTCCACTGAAAATGTTATAAAATCAAAACTGCACCCCAAATTGGTAGAGCCTTGGAATCAAGGGAAATATAGTATATGGTCTGGTGTTTATGACATAATTAAAGGGGAAATGGAGTGAGAGTCTCCTATGTATATTTAAATCTCACCCGTAGTTAACGGTATGGGTAATTGAGATTTCCCTTGTAACTTTTGAAAAAAAGTTGAAAAAGTGGTCCATGAACATTTAACATGTTTCCATTTATTCTCTTGAAGAAAATACTGTATGGACTCCAAACAAAAATCAGTGAAACCTTTTCACCTTGAAGAAATTGGACTCAGTAATGGCTATTCCAATCTGTGTTGAAAAGAGAATAAAAATTAAGGCTTTAATATGTCGCCTATAAAGTTACCAGTCCCACTTATAGTCTCCCCTGATAGAAATGGAGTGTGGAAAGATATGGGTTGACAAAATAAGATGTTGGCTCCTTCTGATTATTAATGTGTTCTAACAGATTCAGCTAGCTAAGTGCAAAATTGTGATACAGTTGCTAGTTTTACTGTGCACTGCATAAATAATACTTCCTATTTGATACAG
Seq C2 exon
ATATGTGGCGGTGACAAACCATTTCTGGCCCCTAATGACCTGCAGACCAAACATCTGGAGCTTAAGGAAGAATCTGTGAAGCTATTTCGAGGGGTAAAGAAGATGGGTGGGGAGGAATTTAGCCGTCGTTACTTGCAACAGTTGGAGACTGAAATAGATGAACTCTACATCCAGTATATCAAGCACAATGATAGCAAAAATATCTTCCATGCAGCTCGTACCCCAGCCACACTGTTTGTTGTCATCTTTATCACATATGTGATTGCTGGTGTGACTGGATTCATTGGTTTGGACATCATAGCTAGCCTATGCAATATGATAATGGGACTGACCCTTATCACCCTGTGTACCTGGGCATACATCCGGTACTCTGGAGAATACCGAGAGCTGGGAGCTGTAATAGACCAAGTGGCTGCAGCCTTGTGGGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014312:ENSBTAT00000019032:11
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:
PF028419=GBP_C=FE(18.0=100)
A:
NA
C2:
PF028419=GBP_C=PD(53.9=47.9)
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:
AATTTAGCAGCCGTGGCAACT
R:
ACCAATGAATCCAGTCACACCA
Band lengths:
342-1415
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development