Sequence
atgc intronic sequence ATGC exonic sequencegtactgttattgattttaattgattctttccaaacaaccggttgtaaaatggctgatattctttttatttttattattttttacgtaccagGTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAAGACATGTTCAGCAACTGGATATTCATAATCATAGTCGTCTCCTCAGTTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0158g00360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os11g04460.1 (Oryza sativa), 3'ss of exon 6
--gtactgttattgattttaattgattctttccaaacaaccggttgtaaaatggctgatattctttttatttttattat----tttttac-------gtaccagGTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAAGACATGTTCAGCAACTGGATATTCAT---AATCATAGTCGTCTCCTCAGTTA
| |||| || ||| | || || ||| ||| || | | | |||| || || || | || || || | | |||||||||||||||||||||||||||| | || ||| ||||||| |||||||||| | || ||||||| ||||| ||||| | |||||| | || ||
ctgaactgata--gatat--atcttttttttaaaaaaaaataatcatgatttggcaagggaatttcttgttctaatgatgatgttctggcaaacgttgtaccagGTATTCAATGAAATAAACAGCAGAGAAATGCAGAAGATCAATGTTTTCCGTGGTATCATCAGCAATTGGATCTTCATTGCAGTCATAGCTGCAACCGTAG---
upper sequence: Vv13s0158g00360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g04220.1 (Oryza sativa), 3'ss of exon 6
---gtactgttattgattttaattgattctttccaaacaacc--ggttgtaaaatggctgatattctttttatttttattatttt------ttacgtaccagGTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAAGACATGTTCAGCAACTGGATATTCAT---AATCATAGTCGTCTCCTCAGTTA
| |||| || || || || || ||| ||| || | | || || || | | || || | | | || | | |||||||||||||||||||||||||||| | || ||| ||||||| |||||||||| | ||| ||||||| ||||| ||||| | |||||| | || ||
cctgaactgata--gagttatcttttttttttaaaaaaaatcatgatttggcaaagggaatttcttgttctaatgatgatgttctggcaaatgttgtaccagGTATTCAATGAAATAAACAGCAGAGAAATGCAGAAGATCAATGTTTTCCGTGGCATCATCAGCAATTGGATCTTCATTGCAGTCATAGCAGCAACCGTAG---
upper sequence: Vv13s0158g00360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G01360.1 (Glycine max), 3'ss of exon 7
---gtactgttattgattttaattgattctttccaaacaacc--ggttgtaaaatggctga-tattctttttatttttattattttt-----tacgtaccagGTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAAGACATGTTCAGCAACTGGATATTCATAATCATAGTCGTCTCCTCAGTTA
| ||||| | | ||| ||| | | | || || || | | | | | | | || | || | ||||| | || || |||||||||| || |||||||||||||| |||||||||||||||||||| |||| |||||| |||| |||| | || | || | | | | | | |
ttggccttgttacttacttt--ttggtcatgttcatgcatcctgaggcacacactaaccaactcttgtcattggaaacaatatttctgtcattaactaatagGTATTCAACGAGATAAACAGCCGTGACATGGAGAAGATAAATGTTTTGCAAGGCATGTTGAGCAGCTGGGTTTTTCTGATGGTCATGGCCGCAACTATAG
upper sequence: Vv13s0158g00360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G35970.1 (Glycine max), 3'ss of exon 6
---gtactgttattgattttaattgattctttccaaac--aaccggttgtaaaatggctgatattctttttatttttattattttt-----tacgtaccagGTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAAGACATGTTCAGCAACTGGATATTCATAATCATAGTCGTCTCCTCAGTTA
|| |||||||| |||| | | | || | | || | | | | || | | || | | ||||| | || || |||||||||| || |||||||||||||| ||||||||| | |||||||| |||| |||||| |||| |||| | || | || | | | | | | |
tacttaatgttattg-ttttggtcatgttcatgcatcctgagcctgaggcacacactatgttctgtcattgaaaaacaatatttgtgtgattaattaatagGTATTCAACGAGATAAACAGCCGTGACATGGAGAAGGTTAATGTTTTACAAGGCATGTTGAGCAGCTGGGTTTTTCTGATGGTGATGGCCGCAACTATATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|37188333|gb|CF607682.1|CF607682EST: CCAGTAAAATTCTTAACACATTCATATTCAATGCCTTCGTCTTTTGCCAG GTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAA
genomic: CCAGTAAAATTCTTAACACATTCATATTCAATGCCTTCGTCTTTTGCCAGgtactgttat ... tacgtaccagGTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAA
EST:
gi|30252763|gb|CB970314.1|CB970314EST: CCAGTAAAATTCTTAACACATTCATATTCAATGCCTTCGTCTTTTGCCAG GTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAA
genomic: CCAGTAAAATTCTTAACACATTCATATTCAATGCCTTCGTCTTTTGCCAGgtactgttat ... tacgtaccagGTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accggttgtaaaatggctgatattctttttatttttattattttttacgtaccagGTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAAGACATGTTCAGCAACTGGATATTCATAATCATAGTCGTCTCCTCAGTTA
ggctgat putative branch site (score: 4)
ttctttttatttttat CT-rich tract
taaaatggctgatatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgttattgattttaattgattctttccaaacaaccggttgtaaaatggctgatattctttttatttttattattttttacgtaccagGTATTCAATGAAATAAACAGCCGTGATATGGAGAAGATAAATGTTTTCCAAGACATGTTCAGCAACTGGATATTCATAATCATAGTCGTCTCCTCAGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC