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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgttaaatctacacaaatttgcagaaggacattctttcttctatgtgactttacacaaacttgattatgaggagaggcacaaataactcaaat...

Basic information

species Vitis vinifera
transcript Vv04s0008g00650.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g00650.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA17G34990.1 (Glycine max), 5'ss of exon 9
TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgttaaatctacacaa-atttgcagaaggacattctttcttctatgtgactttacacaaacttgattatgaggagaggca--caaataactcaaat
||| || |||||||  |||||| ||||||||||||||||||||||| || | | |     |   |  || ||    |  |  | |  | |  |  |  |||| | |     || |   ||      || |      ||  |     
TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatatcagcatcatgtaccatgtgattcataagctccagtttctttagctacttgagattgtttttaacctgccagttggtagtttggtattttg---

upper sequence: Vv04s0008g00650.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA14G10520.1 (Glycine max), 5'ss of exon 9
TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgttaaatctacacaa-atttgcagaaggacattctttcttctatgtgactttacacaaacttgattatgaggagaggcacaaataactcaaat
||| || |||||||  |||||| ||||||||||||||||||||||| || ||| |     |   |  || ||    |  |  | |    |  |  |  |||| | |     || |   ||  |   || |    |       ||
TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatgtcatcatcatgtaccatgtgattcataagctccagcttctttagctacttgagattgtttttaacctgctgtttggta-gtttggtattgat

upper sequence: Vv04s0008g00650.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA17G34990.2 (Glycine max), 5'ss of exon 8
---------------------------------------------------------TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgttaaatctacacaa-atttgcagaaggacattctttcttctatgtgactttacacaaacttgattatgaggagaggca--caaataactcaaat
                                                         ||| || |||||||  |||||| ||||||||||||||||||||||| || | | |     |   |  || ||    |  |  | |  | |  |  |  |||| | |     || |   ||      || |      ||  |     
CAGTGGATCCATTGTTCCATTGTCTGTTTTAATTTTCAAATGTGTTTGTGTGTTCAGTGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatatcagcatcatgtaccatgtgattcataagctccagtttctttagctacttgagattgtttttaacctgccagttggtagtttggtattttg---

upper sequence: Vv04s0008g00650.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT2G25910.2 (Arabidopsis thaliana), 5'ss of exon 9
---TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgttaaatctacacaaatttgcagaaggacattctttcttctatgtgactttacacaaac--ttgattatgaggagaggcacaaataactcaaat---------------------------
    ||||| ||||| |||||||| || ||||| |||||||| |||||||||||  |   || | |    |   ||    ||      |||   ||| |  ||||  |  |    ||| |      || ||    ||||||   |                              
CAGCGCGGAAATTCTAATTGGAGGGGCAAAGGGTCCACCTGATAAGgttagtcttat---tccataggggtacacaatctgaacacaattccattatttagctttgaatgagagattggtggaaccgaaagatgtaaataaggtagtgtttatgtggaaacgggttttggtgcag

upper sequence: Vv04s0008g00650.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT2G25910.1 (Arabidopsis thaliana), 5'ss of exon 9
TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgttaaatctacacaaatttgcagaaggacattctttcttctatgtgactttacacaaac--ttgattatgaggagaggcacaaataactcaaat---------------------------
 ||||| ||||| |||||||| || ||||| |||||||| |||||||||||  |   || | |    |   ||    ||      |||   ||| |  ||||  |  |    ||| |      || ||    ||||||   |                              
CGCGGAAATTCTAATTGGAGGGGCAAAGGGTCCACCTGATAAGgttagtcttat---tccataggggtacacaatctgaacacaattccattatttagctttgaatgagagattggtggaaccgaaagatgtaaataaggtagtgtttatgtggaaacgggttttggtgcag

Mapped 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|83275821|gb|DV939829.1|DV939829
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|156737847|gb|EV241968.1|EV241968
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTAAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|33409610|gb|CF215237.1|CF215237
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|110722833|gb|EE099455.1|EE099455
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|30129707|gb|CB915046.1|CB915046
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCG
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCG
EST: gi|110388273|gb|EC953007.1|EC953007
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|26267080|gb|CA818143.1|CA818143
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|71883347|gb|DT032402.1|DT032402
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGA
EST: gi|110365546|gb|EC928709.1|EC928709
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|110373103|gb|EC937314.1|EC937314
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|110416192|gb|EC982154.1|EC982154
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|26265140|gb|CA816203.1|CA816203
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCCCCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|110385784|gb|EC950339.1|EC950339
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|32246079|gb|CD711898.1|CD711898
EST:     CGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: CGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|110723073|gb|EE099967.1|EE099967
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTAAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|30128917|gb|CB914256.1|CB914256
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|30321844|gb|CD005106.1|CD005106
EST:     GCAATGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTAAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: GCAATGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
EST: gi|110367167|gb|EC931093.1|EC931093
EST:     TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAG                         GTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA
genomic: TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgt ... gttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGGAGATTCTCATTGGAGGTGCCAAGGGCCCACCTGACAAGgttagtctgttaaatctacacaaatttgcagaaggacattctttcttctatgtgactttacacaaacttgattatgaggagaggcacaaataactcaaat

-  GGAGAT
- - - - - - - TTGGAG
- - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaataa