BtaINT0135563 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007650 | SLC38A11
Description
Bos taurus solute carrier family 38, member 11 (SLC38A11), mRNA. [Source:RefSeq mRNA;Acc:NM_001031760]
Coordinates
chr2:31391774-31392741:+
Coord C1 exon
chr2:31391774-31391943
Coord A exon
chr2:31391944-31392623
Coord C2 exon
chr2:31392624-31392741
Length
680 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
ATTTTTATATACTGAAATAGAGC
3' ss Score
4.14
Exon sequences
Seq C1 exon
TGGGGCGAATTGCTTCCGCAGAGCCTCAACCCGGCTCTCTCCCGGCGCCCTGACGCCGGGCTCGGAGGTCGCGGAGGAGTCGAGGACCCGCGCCCGCGAACCTTCCACCCGCGGAAGACCCGGGTGCAGCCATGGGCTACCCCGGGCAGAGGCCCGTCATCCCGCCGCAG
Seq A exon
GTAAAACTGGAGATGGGACAGGTTCTGAAGGCAGGACCGTTCAAGTTTCCTTCACCTGCAGGAGTTCAGCTGCCTTTACCTGCAGGAGTTCAGCTGCCTTCACCTGGGGTCTTGATTTAGCACCAAGATTGAGGGCAGGAATAGAAGGGAGCGGAAGAGGATGAGATGATTAGATAACATCACCTACTCAATGGACGTTAAGTTTGAGCAAACTGGGAGATAGTGGAGGGCAGGGAAGCCTGGCGTGCTGCTGTCCATGGGATGGCAGAGTCAGACACGACAGCGACTGAACAAGGTTCTCCAGGAGAAAAAAATTTGCCTTAATCTTTTTTTTTTTTTTTGGTCAGGCACTTTTCAATATAACCCCTTTCGTTTCACACACACACACACAAATCACATTTGCTCCCTGGGAGATCCTGTACTCTAGGAGTTCATGCAGCAGTCCACGAACTTGGCACAGCTGTAATCAGCACATTTTAGGATGGAGTGTGTTCAGAAGCTCTGCATTACTAGATATTATTGTTACTTTTTATTATTATCTTCATCTTCTTACCGTTATTGACATCACTTGTTATTATTACTAATATCGTGTTAGTCTCCTACATTGCGTATTTATTTTAAAATGTTCAAAATTTTTGATCTAAGTCTTTATTCAATCGCATTTTTATATACTGAAATAG
Seq C2 exon
AGCCATCGAGATGACAGAGAAACCCTGGTTTCTGAACATAAGCACAAAGGGAAAACTTGTCGTCAGTCTGCTGCCGTTTTTAATGTTGTCAACTCAATTATAGGGTCTGGTATAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007650:ENSBTAT00000010065:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.769 A=NA C2=0.375
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0149013=Aa_trans=PU(42.3=55.0)
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:
TGGGGCGAATTGCTTCCG
R:
ACCAGACCCTATAATTGAGTTGACA
Band lengths:
281-961
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]