BtaINT0142025 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002658 | STAM
Description
Bos taurus signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 (STAM), mRNA. [Source:RefSeq mRNA;Acc:NM_001076842]
Coordinates
chr13:32421079-32422817:+
Coord C1 exon
chr13:32421079-32421174
Coord A exon
chr13:32421175-32422670
Coord C2 exon
chr13:32422671-32422817
Length
1496 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TTTTTTTCTCTATTTTTCAGGGT
3' ss Score
12.63
Exon sequences
Seq C1 exon
CTTCTAGGAGCATGTGTATCAAACTGTGGCAAAATTTTTCACTTAGAAGTATGTTCGAGAGATTTTGCTAGTGAAGTAAGCAACGTATTAAACAAG
Seq A exon
GTAAAGAACATTATTTCCAGAAATGAATTAAGACTGTCTTCTTTCTTCATGTATTTTACATGTATTTTATTGTTCAATTCTTCACATTTTTAAATCACAAAGGACTAGTCTGTGTTTTTTTGTTTTTGTTTTTTTAGCTCTTTCTAGGCTATGTCTATCCCATGTATATCCATGTTAGGTTTGCTGAGGAGACTACGTATTTATATAACTTGGAGCATTGGTTTTGGTGAAGCCAAATTAGGATACATTTAACCTTTTTTCTTCATCAGTCCTTTTTTCTGATGAAAAATATGTGCATTTTTCTATCTGATGAAAAGGTACCAGTTTATTTTGGGCACAGTTCTTACTGTGCTTTTTTAGTCACAGAGGTCATCTGCTTAACAAAATGTAAGGCATTCAAATCCAGCAGTTGAAGGAATTTTTAAAATTTAATTACTAAGTAATATCTAAGTTTTCCCAGTAAAAATTCATGCATTCTAAAGGTAGTTATCTCTGGCCTTTCTTGGTGGTGGGTGGAGTAATTATTAAGAAAAATTATTTTTAATGTTAAAAGGGGAAATGCTTCATGTTTTTTTGGGAAAAAAGAGCATTTCCAAATTTTAGTAGGAAACAGTAAAGAAGTGAGATAATTTAAAATGCTGGACTTCTTTTAATACACTATGGTATGTGATAATTTTTTCCTGTGCTACTTTATTCAGTTATTTAGCTATATTGTATTTAAGGTTTTTTGTTTGTTTTTTTTTTTTTTTACTAATTCTTTACCATTCTTTTGATGTCTTGAATGTCCATTCAAAATGTACAGCTATTTATGAAGAGATTCTAATATAATATTTTCTTTAATTGAAGATGTGTACTCAGTACTTAGTAATATAAACAACTACATTGAAAGGCAAGCAGTTGCATACAGGAGAAAGAACTTCACTTTATTTTACATATATTTTATAGTGAACTTACTGGTTTTATACTTAAGAGGGAGATGCTGTTTTGAAGAAATGAGGTTTCCAGGAATATGGACAGTACTGGGCCTCAAGATAATTAAGTAATTGGAGGAAAACACAGTCATGCATATAAAAAATCAGGAATTAGAAATAAAAGAACTGTATTATTTATTCTCTTTTCCAACTTATTTTTTTATTGGTCTGAAAAAAAGAAAATAGATTTTCCTGTCTTCTTCATATGCAGTAAAATATGAGTGAGTAAAATACTCTGACATACTCTTAGTCTTAAAATACTCTGAAAAGTCATATCTTTCTGGCCTCCAAAATAAGTAACTGTATATCTAATGTTTTGATTTGATGTGGCGTATGTGATGGTATCATCTATTTTTTTTCCATAATATGAAAATAAAAGTAGCTTATTTCTAGTAACCATCTGTGTTTTCTTATGTGTCACCTATAGCTAGGGATACTTTATGATTTAAAGAGAGATCTGAAATACTGTATTAAATCATTAACCAGAAAGTGCTTTTTTGTTAAATTTTTTTCTCTATTTTTCAG
Seq C2 exon
GGTCATCCTAAAGTATGTGAAAAATTGAAGGCTCTTATGGTTGAATGGACGGATGAATTCAAGAATGATCCACAGCTCAGTCTGATATCAGCAATGATTAAGAACCTGAAAGAACAGGGTGTTACATTTCCCGCTATTGGCTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002658:ENSBTAT00000003441:4
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=0.010
Domain overlap (PFAM):
C1:
PF0079014=VHS=FE(23.0=100),PF136461=HEAT_2=FE(25.0=100)
A:
NA
C2:
PF0079014=VHS=PD(28.9=79.6),PF136461=HEAT_2=PD(29.0=73.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCATGTGTATCAAACTGTGGC
R:
GCCAATAGCGGGAAATGTAACAC
Band lengths:
230-1726
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development