RnoALTD0020094-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000021910 | Nkx2-6
Description
NK2 homeobox 6 [Source:RGD Symbol;Acc:1306149]
Coordinates
chr15:51034589-51038704:+
Coord C1 exon
chr15:51034589-51034689
Coord A exon
chr15:51034690-51034693
Coord C2 exon
chr15:51037343-51038704
Length
4 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGC
5' ss Score
5.66
3' ss Seq
TTCCTTCCTTGTGACTTTAGAGA
3' ss Score
6.67
Exon sequences
Seq C1 exon
AAGGTCTGAGAGCTTCGACACAGTACAGACAGAAGCAACCCCTTTTCTGTGCACCTGGGAGACAGTCCTAGAGATGGACTCAAATCTTGTGAGGGAGCCGA
Seq A exon
GTAA
Seq C2 exon
AGACTCCCCCGGGCACAATCTCCCCACTTGGAGTCGAGAACCTGATGATGGAGCATGGCGTGGGCAACCGGAGCGACGACCCGCGCCGAGCTGGCCCTGTTCCGACCGTGACCCGGCCACGGCGGAAGCCCCGCGTGCTATTTTCGCAGGCCCAGGTGCTGGCCCTGGAGCGGCGCTTCAAGCAGCAGCGATACCTGTCTGCGCCGGAGCGTGAGCACTTGGCCAGTGTGCTGCAGCTCACGTCCACGCAGGTCAAGATCTGGTTCCAAAACCGGCGCTACAAGTGCAAGAGACAGCGCCAGGACCAGACCCTGGAACTGGCGGGCCACCCACTAGCACCGCGCCGGGTGGCAGTGCCCGTACTTGTACTGGACGTCAAGCCCTGCCTAGATCCCGACAGACACGCATTCCCGAGTCCCTACGCAACCACCGTGCTCTACTCCTGCTTCAGCAGCTACACAGGCACTCCCTACAGCGCTAGCTATGCGGGCCGCTACACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021910-0-1,1-1-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref, Alt. Stop)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.397
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=27.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
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:
AACCCCTTTTCTGTGCACCTG
R:
GTTCTCGACTCCAAGTGGGGA
Band lengths:
106-110
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]