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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACTACTGGAGGCTTCCCAAGGACGCAACCCTGAAGGATGTTATAACTGTGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactgctagccttctccatttcaatgcatgtttttggtttttcttctgattttggttgaatttcttatgtactttgttctgtttgaatgagccaa...

Basic information

species Vitis vinifera
transcript Vv12s0142g00430.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0142g00430.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G07700.1 (Glycine max), 5'ss of exon 3
AGACTACTGGAGGCTTCCCAAGGACGCAACCCTGAAGGATGTTATAACTGTGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactgctagccttctccatttcaatgcatgtttttggtttttcttctgattttggttgaatttcttatgtactttgttctgtttgaatgagccaa------
|||||| ||||||||||||||||| || |   |||| ||||||||||| || || ||||||||||| ||||||||||||||||| || ||||||||||||||||||  |  |     || |    | ||| ||| |||||| || |  |     ||      |   | ||| |  |  |    |   ||  ||   | ||      
AGACTATTGGAGGCTTCCCAAGGATGCCAGATTGAAAGATGTTATAACAGTCATTCGTGCTGATGAGGCTCACCATCGAGATGTGAACCATTTTGCTTCTgtgagtgttctt---tctcactcgcttaat-catctttttgcttgtcttaaaagttaaaacagcgatgcttcttcagctccaccaactt--atccactaaaattgt

upper sequence: Vv12s0142g00430.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G07690.1 (Glycine max), 5'ss of exon 3
AGACTACTGGAGGCTTCCCAAGGACGCAACCCTGAAGGATGTTATAACTGTGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactgctagccttctccatt-----tcaatgcatgtttttgg-------tttttcttctgattttggttgaatttcttatgtactttgttctgtttgaatgagccaa
 ||||||||||||||||||||||| ||||| || ||||||||| | |||||||| || |||||||| ||||| ||  | ||||| || || ||||||||||| |||     |  | |     | |      |||   |  || || |       || |||  |  |||||  || ||    ||    |  || |  | ||            
TGACTACTGGAGGCTTCCCAAGGATGCAACTCTCAAGGATGTTGTCACTGTGATTCGCGCTGATGAGGCTCATCACAGGGATGTTAACCACTTTGCTTCTgtaagtttccttttcgtctcataatggacaacaacaaaaattgttaggaacacattcttcaacatattttttttaaagaaatttaacatattttcttatt------------

upper sequence: Vv12s0142g00430.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G64210.1 (Arabidopsis thaliana), 5'ss of exon 4
AGACTACTGGAGGCTTCCCAAGGACGCAACCCTGAAGGATGTTATAACTGTGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactgctagccttctccatttcaatgcatgtttttggtttttcttctgattttggttgaatttcttatgt--actttgttctgtttgaatgagccaa-----
 || || |||||  | || || || || ||  |||| |||||| |||| ||||| ||||||||||||||||| |||||||||||||| |||||||||||||||||| ||   |       || |||      || |||||       || | || |||  |  | ||  |   ||  | || | |    || ||  | | ||     
TGATTATTGGAGATTGCCTAAAGATGCTACGTTGAAAGATGTTGTAACGGTGATTCGTGCTGATGAAGCTCATCATCGAGATGTCAACCATTTTGCTTCTgtgagt-ctaaaacaacaaccctttt------attttttttccaaaactcccgagtttcatacatttcttcgggtccatttcggtgatattaaaataacaaatgata

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|32246117|gb|CD711936.1|CD711936
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
EST: gi|30132579|gb|CB917918.1|CB917918
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
EST: gi|30133960|gb|CB919299.1|CB919299
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
EST: gi|110403191|gb|EC964495.1|EC964495
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
EST: gi|110705975|gb|EE083437.1|EE083437
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAAGAAATTGAATGAGGCACCANCCCCTATTGG
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAA-GAAATTGAATGAGGCACCAGCCCCTATTGG
EST: gi|110383282|gb|EC947645.1|EC947645
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
EST: gi|110698477|gb|EE076023.1|EE076023
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
EST: gi|30127808|gb|CB913147.1|CB913147
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
EST: gi|71875006|gb|DT024061.1|DT024061
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
EST: gi|30125181|gb|CB910520.1|CB910520
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
EST: gi|110404402|gb|EC969403.1|EC969403
EST:     TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCT                         GATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT
genomic: TGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactg ... tgctctgcagGATATTCATTTCCAGGGAAAGAAATTGAATGAGGCACCAGCCCCTATTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACTACTGGAGGCTTCCCAAGGACGCAACCCTGAAGGATGTTATAACTGTGATCCGTGCTGATGAAGCTCACCATCGAGATGTCAATCATTTTGCTTCTgtgagtactgctagccttctccatttcaatgcatgtttttggtttttcttctgattttggttgaatttcttatgtactttgttctgtttgaatgagccaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctcc