Sequence
atgc intronic sequence ATGC exonic sequence...cttgattttctctctgcatgctgctgcattctcctttttttaagagtcttttcatctcatttaaatgtgacttgaaaatttgatatggctactttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g10700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os09g28560.1 (Oryza sativa), 3'ss of exon 2
-----cttgattttctctctgcatgctgctgcattctcctttttttaagagtcttttcatctcatttaaatgtgacttgaaaatttgatatggctactttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA
||| | | ||| | | | | || || | | | | ||| | || ||| | | ||| | | | | | ||| ||||||| |||||| || || |||||||| ||||| ||||||| | ||||| ||||| || || || |||||||||||||| |||||||| |||||||||||
ctcttctttaagatgtcttt-taggttatagccttataggtacctgtaaagttgagtgatgctttttctcttt-actgaagcactctcttttgctg---tttcagCGGAAACTTCTGGTACCACTGTTACATTTGTAGTAATAGATGAGTGGGTTGTAACGGTAGCATCAGTTGGTGATTCACGTTGCATACTAGAATCTGCTGA
upper sequence: Vv18s0001g10700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g27780.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------------------------------------------cttgattttctctctgcatgctgctgcattctcctttttttaagagtcttttcatctcatt-taaatgtg-act----tgaaaatttgatatggctactttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA
| | | | | | | | | || ||| | || | | | | || || | || ||| || ||| | | | | | |||||||| ||||| || ||||| || |||||||||||||| |||||||| || ||||| || || ||||| ||||| || || || || |||||||||||
gtattattctttcactaagctgataacgatttagaggatgtgcatgtaatttagaggcttttagttttctttgttcatattctcccccttttggacaaatatctttctgatttatgaatacatgatcagtgttgttatacacttgcactgcggtgtaaactgattgttaccatgttttcagCGGCGCGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCCCGCTGTATCCTAGAATCTGCTGA
upper sequence: Vv18s0001g10700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G077960_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------------------cttgattttctct-----ctgcatgctgctgcattctcctttttttaagagtcttttcatctcatttaaatgtgacttgaaaatttgatatggctactttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA
||| | || || |||||| || | || | || | | | || ||| ||| | || || || ||| | | | | |||||||| | ||||| || ||||| || |||||||||||||| |||||||| || ||||| || || ||||| |||||||| ||||| || |||||||||||
gtattataaatgggatgccaggtctgcctgtcttttaaccatccaaaagcaaattatttctcaatggatttgcaatgttcacaggagcatacaccatttgctgtttactgtggattgcatggtgttagcctcctatattgccatgggatcttcagactc-tttcactgcga--tgtaaactgactgttataatgttttcagCTGCACGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCACGATGCATTCTAGAATCTGCTGA
upper sequence: Vv18s0001g10700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G150213_T04 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------------------cttgattttctctctgcat-----gctgctgcattctcctttttttaagagtcttttcatctcatttaaatgtgacttgaaaatttgatatggctactttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA
||| | || | || || | | ||||| | | | | | | ||| ||| | ||||| || ||| | ||| | |||||||| | |||||| || ||||| || |||||||||||||| |||||||| || ||||| || || ||||| |||||||| || || || |||||||||||
gtattataaatgggttgtcagatctgcctgtccgttaaccattcaaaagcaaattatttctcagtggatgtccaatgtttacaggagcatacagcatttgctgtttaccatggatagaggatgattttagcctcctatatatcatggagtcctcagactgtttcactgtga--tgtaaactgactata---atgttttcagCTGCACGTTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCACGATGTATTCTAGAATCTGCTGA
upper sequence: Vv18s0001g10700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G135444_T01 (Zea mays), 3'ss of exon 2
-cttgattttct-----ctctgcatgctgctgcattctcctttttttaagagtcttttcatctcatttaaatgtgacttgaaaatttgatatggctactttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA
| || | | || | | | | | ||| |||| | |||||||| | || |||| | | | ||| | |||||||||| |||||| || |||||||| || ||||| |||||||| | ||||| || ||||| || || || ||||||||||| |||||||| |||||||| ||
attagaacatatgagaacttcatttatggtccaaaatttcctttgttaactgccttttcatgt--ttcaaatatttatggggcgttttct----tcactttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTGTGACTGTAGCATCTGTCGGTGATTCACGTTGCATACTAGAATCTGCCGA
upper sequence: Vv18s0001g10700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G052699_T02 (Zea mays), 3'ss of exon 2
------cttgattttctctctgcatgctgctgcattctcctttttttaagagtcttttcatctcatttaaatgtgacttgaaaatttgatatggctactttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA
|| |||| | | ||| | ||| | | ||| | | | | |||| || | || || | | ||||| ||||||| ||||||| |||||||| || ||||| |||||||| |||| ||| | |||||||| || ||||||||||| || || |||| || ||| |
ctactactagattatactgccatatgttttaccatgtggactatgacgagaaccatctttacgcattactatatcgt------atctgttgggttgtcttttacagCACGTTCTTCAGGGACAACTGTGACATTTGTCATAATAGATGGATTGGTCATCACTGTTGCATCAGTTGGTGATTCCCGTTGTGTACTACAAGCTGAAGG
upper sequence: Vv18s0001g10700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------cttgattttctctctgcatgctgctgcattctccttt-ttttaagagtctttt--catctcatttaaatgtgacttgaaaatttgatatggctactt---tttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA
|| ||| || | | || | || || | | || | | |||| | ||| | || | || | ||| || || | ||| |||||||| | || || ||||| ||||| || ||||| ||| |||||||||||||||| | |||||| || || ||||| || || ||||||||||| |||||||
gtatgaacttatcaatgaaaaaccttgtgatgtgattcaagtcccaagagggtgaactcgtctgtgtctttatattcttatatcattctggtgaaggctatgtttgaggttttat-tgttttcttgcatttcagCAAGGACGTCTGGAACGACTGTAACTTTTGTCATAGTAGAAGGATGGGTGGTGAGTGTTGCATCTGTAGGTGACTCTCGTTGCATACTTGAGCCTGCTGAMapped 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|110398997|gb|EC965481.1|EC965481EST: TTGGTTGCAGGGTTTGTTAAGACAGATATAGATTTCCAAGAGAAAG CACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGG
genomic: TTGGTTGCAGGGTTTGTTAAGACAGATATAGATTTCCAAGAGAAAGgtatgaataa ... actttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGG
EST:
gi|161713118|gb|FC064293.1|FC064293EST: GGCTTTGGTTGCAGGGTTTGTTAAGACAGATATAGATTTCCAAGAGAAAG CACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGG
genomic: GGCTTTGGTTGCAGGGTTTGTTAAGACAGATATAGATTTCCAAGAGAAAGgtatgaataa ... actttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttttcatctcatttaaatgtgacttgaaaatttgatatggctactttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA
atttgat putative branch site (score: 5)
ctactttttc putative PPT
ttgaaaatttgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgattttctctctgcatgctgctgcattctcctttttttaagagtcttttcatctcatttaaatgtgacttgaaaatttgatatggctactttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA
- - - - tctctct
- - - - - - - -gcatgct
- - - - - - - - - - - - -gcattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatggct