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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttttttttaatgttgggagatccaataaatactgtttataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca...

Basic information

species Vitis vinifera
transcript Vv11s0052g00320.t01
intron # 30
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 5'ss of exon 11
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttttttttaat--gttgggagatccaataaatactgtttataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca-
| || ||||| ||||| || ||||| || ||||| |||||||||||||| ||||||||||||||||| || || ||| |  |||| || ||||| || | || | |     |  ||       |      | |||| |  || || |    ||| |    ||  |  | | |    ||      | ||| |  | |    || 
TTCTTTGGGTCAATCTCATTATGGACACACTTGGTGCACTTGCATTGGCTACTGAACCACCAACAGACCAACTTATGAAGCGGCCACCTGTTGGACGGAAgttagtacacctgaaaccaacccgtgctcactataattcttgattgtc--ttaaatttgtaaaggaataacaaaattctaacatgctttcacatttaacacag

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttttttttaatgttgggagatccaataaatactgtttataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca------
| || |||||||| || |||||||||||||| || || |||||| |||| || |||||||| || || || || ||||| || || ||||||||  ||||||  | || | | |  | |||   ||      || |    |   |    |  |  || ||||   |      |     |  |||          | |  |      
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtt-tgttctctgtgttcttgctggac-----aactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: GRMZM5G893864_T01 (Zea mays), 5'ss of exon 7
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttttttttaatgttgggagatc-caataaatactgtttataaacta-agtgga---aaattgggtcagatctgtccctggaggtttgaattgtgcttca
| |||||||||||||| |||||||| || || || || ||||| ||||| |||||||||||||||||||| || |||    |||| |||||||| || |||| |    | |||| || |||    ||    || | |    || ||   ||  | | |    |   ||  |      |  ||           || | ||     
TTCTCTGGGTTAATCTCATCATGGACACACTCGGTGCTCTTGCTTTGGCTACTGAACCACCAACAGATCAACTTATGAGGCGGCCACCAGTTGGACGGAGgttagaagtctttttattttgaatcattattatgagtgtgattgattgcctccactaggcctagcctgcatgcagcataacctaatccaccataaatatg-----

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: GLYMA17G06520.1 (Glycine max), 5'ss of exon 30
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgt-aattttttttttaatgttgggagatccaataaatactgtttataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca------
| |||||||| ||||||||||||||||||||||||||| | || ||||| |||||||||||||| |||  ||||||| |      ||||   |||||||||| ||||||||||  |   ||      |   || ||  |     |   |   || | | |||   || | |   |  |   | | | |  ||  | |   |      
TTCTCTGGGTAAATCTTATCATGGATACTCTTGGAGCATTAGCCTTGGCAACTGAACCACCAACTGATTCCCTGATGGATCAAAGTCCAAAGGGTCGAAGgtcaattttttttccatcatttt----ttttatgaaagcaagaaaattaaagagagaagaataatgtaaaa---gatcaaagtgatatatatccttcacaaaatacc

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 27
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttttttttaatgttgggagatccaataaatactgtttataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca------
| || ||||| |||||||||||||||||||| |||||||| ||  |||| |||||||||||||| |||||||| ||| |  |  | ||||| |||||||||| |   ||||| |  | ||  ||     | |   ||||    | | |  | |        |  ||  | | | |   || ||| ||| |  ||| ||        
TTCTTTGGGTAAATCTTATCATGGATACTCTGGGAGCACTAGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGATCCCCAGTGGGTCGAAGgtcagagtttttat--ttttctgattattattgggtact----acagatcatggcatttcatttgtttgctatattattgtagggttgcacagtgtttggaaaatt

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: GLYMA13G00420.1 (Glycine max), 5'ss of exon 28
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgt-aattttttttttaatgttgggagatccaataaatactgttta--taaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca-
| |||||||| ||||||||||||||||||||||||||| | || ||||| |||||||| ||||| |||   |||||| |       ||    |||| ||||| |||||||||   |   ||         ||| ||  ||    |  ||||   ||  ||| |  |    |||||              |  |        || 
TTCTCTGGGTAAATCTTATCATGGATACTCTTGGAGCATTAGCCTTGGCAACTGAACCGCCAACTGATTCTCTGATGGATCAAAGCCCTAAGGGTCAAAGgtcaatttttttcccatcatttt----cttaatgaaagctaggaaattaaagagagaagaataacgcacaagatcaaagtgatatatccttcacaaaataccaa

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: GLYMA09G06890.1 (Glycine max), 5'ss of exon 27
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgt---aatttttttttt----aatgttg--ggagatccaataaatactgt----ttataaactaagtggaaaattgg-gtcagatctgtccctggaggtttgaattgtgcttca
| || ||||| |||||||||||||||||||| ||||| || ||  |||| |||||||||||||| |||||||| ||| |  |  ||||||| ||||||||||   ||||||| ||||    | | ||   || ||   |   | || |||    ||  | | |   ||||||||| | ||||   | ||   ||||      |           
TTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAGgtcagaatttttatttttctgattattattggggacttatatattattgtagggttgcacagtgcttggaaaattagtgtcaacacagt---tggaaagccaa-----------

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: AT5G57110.2 (Arabidopsis thaliana), 5'ss of exon 29
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttttttttaatgttgggagatccaa-taaatactgtttataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca---
| |||||||||||||| || ||||| |||||||||||| | || ||||| ||||||||||| || |||||||| |||   ||||||||||||||  ||| ||| | ||||||      |       || || | ||||     | |    |  || || | | |  | |    | ||  |    | ||  | |    ||     
TTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAAAgtactgttttttccgccttctctcattcaaacttaataaaacatttggtttt-gtagaca-tagacttattgttatctttctttgcttcgacttctttttgcag

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 29
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgta--attttttttttaatgttgggagatccaataaatactgtttataaactaagtg---gaaaattgggtcagatctgtccctgga---ggtttgaattgtgct-tca-
|||| ||||| |||||||| |||||||||||||| || ||||| || |||||||| |||||||| |||||| | ||| |  |  | || |||||  |||||||  | || || |   |  |  | |       ||| |  |||| |   |   ||||     |  ||   |   || ||  |    |   | |||   || |||| ||| 
TCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAAGgtaccacttcttatcagacttgagcatgcgtgttaagtcttgttcaactatagagtgctctcagtttctcttcaatttgcacaataattggatttatcttttgctctcag

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 24
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttt---tttttaatgttgggagatccaataaatactgtt-tataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca
| || ||||| |||||||| ||||||||| | ||||| || || || |||||||||||||| |||||  || | ||| | ||||| || || || || |||| |        | | |  |  | |       |||   | |  || | |    | ||                                               
TGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAGgttagacacgggtgtcttctactcgagttcttaatgcgtgcatttgttttgtttcag-----------------------------------------------

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|30299117|gb|CB975911.1|CB975911
EST:     ACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAG                         GGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG
genomic: ACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaatttttt ... catttctcagGGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG
EST: gi|30299189|gb|CB975983.1|CB975983
EST:     ACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAG                         GGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG
genomic: ACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaatttttt ... catttctcagGGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG
EST: gi|30299258|gb|CB976052.1|CB976052
EST:     ACTGAACCACCAACAGATCCCCTGATGCACAGGCCTCCAGTTGGTCGAAG                         GGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG
genomic: ACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaatttttt ... catttctcagGGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG
EST: gi|110727598|gb|EE104541.1|EE104541
EST:     ACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAG                         GGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG
genomic: ACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaatttttt ... catttctcagGGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG
EST: gi|71883815|gb|DT032870.1|DT032870
EST:     ACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAG                         GGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG
genomic: ACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaatttttt ... catttctcagGGAACCATTGATAACAAATATCATGTGGAGGAATTTGTTGATTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttttttttaatgttgggagatccaataaatactgtttataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggaaaa