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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattattctctatctctctactaagataaatacccgtgttttttgtatgttttcttttgttgctaagaaaaaatatgaaaaccaagttggtctattt...

Basic information

species Vitis vinifera
transcript Vv15s0046g02170.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os01g12560.1 (Oryza sativa), 5'ss of exon 3
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgtt-gattattctctatctctctactaagataaatacccgtgttttttgtatgttttcttttgttgctaagaaaaaat--atgaaaaccaagttggtctattt
|||  | || |||||||| || |||||||| |||||  ||||||||||  | | |||||| |||||||| || || |||||||| ||||||||||||||||||   ||||||  |||   || ||       | | |    | | | |||   ||||| |     | | |||  ||     |   | | |   || |   |  
TGTGTTGGAGTGTGTGCCAGCTCCTGTGGCAGCTGCTGCAACATCAGCATTGCAAATCCCAACCATTGGAATTGGTGCTGGACCATTCTGCAGTGGACAGgttcagttattcagtatacttc-acagttcacacttctacagatatatgttcattttcctcaacagtttagattaagccagttgtatctattctgattctt--

upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G010596_T01 (Zea mays), 5'ss of exon 3
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattattctctatctctctactaagataaatacccgtgttttttgtatgttttctt-ttgttgctaagaaaaaatatgaaaaccaagttggtctattt
|||  | || ||||||||||| || ||||| || ||  ||||||||||  |   |||||| ||||||||||| || |||||||| ||||| ||||| ||||||  ||  |   |  |||  ||  | ||  |  |   ||    |   |   ||| ||    | | || ||| | || |||   ||   | |  | |    
TGTGTTGGAGTGTGTGCCTGCTCCAGTGGCAGCAGCTGCAACATCAGCATTGAAAATCCCAACCATTGGCATTGGGGCTGGACCATTCTGTAGTGGCCAGgttcgtttgttctttgctccgtaaaatgaggaggagaagtaagatcacttgctttgctcacagatactgagatacaagatgttgactctggtcatatcca-

upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA07G06950.1 (Glycine max), 5'ss of exon 5
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattattctctatctctctactaagataaatacccgtgttttttgtatgttttcttttgttgctaagaa---aaaatatgaaaacca-agttggtctattt
|||||| || |||||||||||||| || || |||||||| ||  || |||||| ||| || || ||||| || || |||||||| || ||||||||||| |||  ||   ||     |  | | |  |  ||||   | |||| ||   ||||  | |||    |  | |||   |   ||    |   | |||   | | |||
TGTTCTAGAGTGTGTGCCTGCACCGGTTGCGGCTGCAACCACGGCAACCCTTCAAATTCCTACAATTGGAATTGGGGCTGGACCCTTTTGCAGTGGACAAgttagttggcctaa---ttaccattttggaaaatgttc-tgttcttgacatgtactttttgtaagagatgaatgcagcctacattagtgacagtaattttgttt

upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G47310.1 (Glycine max), 5'ss of exon 5
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgt----tgattattct--ctatctctctactaagataa-atacccgtgt-tttttgtatgttttcttttgttgctaagaaaaaatatgaaaaccaagttggtctattt
|||| | || ||||||||||||||||||||||||||  | ||| |||| ||||  || || || ||||| || || ||||  || || |||||||| |||||    || | || ||  |  | | |||| ||  || | || |  | |   ||| ||| |  |    | |  |       | | ||  |  || |  || || || | 
TGTTGTAGAGTGTGTGCCTGCACCTGTGGCTGCTGCTGCTACAGCAGCACTTCAGATTCCAACAATTGGAATTGGGGCTGATCCATTTTGCAGTGGGCAGgtaagttggtcatgctggccttttatctaatactatgatatgcttgagaactttagtaagagtagagtggccg-------agactagcaccactatttttgtgtagt-

upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G39030.1 (Glycine max), 5'ss of exon 3
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattattct--ctatctctctactaagataaatacccgtgttttttgtatgttttcttttgttgctaagaaaaaatatgaaaaccaagttggtctattt
|||| | ||||||||||||||||||||||| |||||    ||| |||| ||||  || || || ||||| || || ||||| || || |||||||| |||||   ||  ||   ||  |  | |||  |     |||  | ||   ||||     ||  ||  |     |       | |  | | |||   |  | | |  
TGTTATAGAATGTGTGCCTGCACCTGTGGCGGCTGCTGTTACAGCAGCACTTCAGATTCCTACTATTGGAATTGGGGCTGGTCCATTTTGCAGTGGCCAGgtaagttggtcatgctgaccttttacctaatattatatgcttgagatttgagaacttcattaagagtggagtggcctagactagagcca--ctattttttcg

upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G46110.1 (Arabidopsis thaliana), 5'ss of exon 2
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgtt------gattattctctatctctctactaagataaataccc--gtgttttttgtatgttttcttttgttgctaagaaaaaatatgaaaaccaagttggtctattt
|||| | ||||| || ||  | ||||| ||||||||  |||| || |||||    || || ||||||||||| || |||||||||||||||||||||||||||      ||  | | ||  ||| ||   |    |   || ||  | |     | |   |||    |   || |||         || |||   ||           
TGTTTTGGAATGCGTTCCACCTCCTGTAGCTGCTGCTGCAACTTCTGCCCTCAAGATACCAACCATTGGCATTGGGGCTGGACCTTTCTGCAGTGGACAGgttttatttgaaaagtttcgttctttccggttttgtgtgtagccaagagacaaatttgcatttctcatacctgttaattgttttcttggaaatgcag-----------

upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G61530.1 (Arabidopsis thaliana), 5'ss of exon 3
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgatt-----attctct--atctctctactaagataaatacccgtgtt----ttttgtatgttttcttttgttgctaagaaaaaatatgaaaaccaagtt---ggtctattt--------------------------------------------------------------------------------------
|||| | |||||||| ||  | ||||||||||||||  |||| || || |||   || || |||||||||||||||||||| |||||||||||||| ||||||  ||     | ||| |  ||     ||   |||  ||||  | | ||    |||  | || ||     || |   |   || ||     |  |  ||||   || || |||                                                                                      
TGTTTTAGAATGTGTTCCACCTCCTGTGGCTGCTGCTGCAACCTCTGCTCTTAATATTCCAACCATTGGCATAGGAGCTGGCCCTTTCTGCAGTGGTCAGgttcgttttgatactctttacattgtcttaacgagagcaataggcttctttcggtttcatgtgcttatacatggtttgattgaataaaccatattctcagttattggcctttttgcatgattaaagagtaagatcagcacaaaaagagtgagttatctacatttctgatcaagtatgtcacatttttcttgtggattcag

upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ15486 (Selaginella moellendorffii), 5'ss of exon 4
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt--ctctat-ctctctactaagataaatacccgtgttttttgtatgttttcttttgttgctaagaaaaaatatgaaaaccaagttggtctattt
 ||||| || ||| | ||  | || ||||||||||| |  || ||  || | |  || || ||||| ||||| |||||||| |||||||||||||| |||||| || |    ||  |   |||   ||  || |  |||    |        | | ||  |||| || | |    |                           
GGTTCTCGAGTGTATACCATCGCCAGTGGCTGCTGCCATCACTTCGTCCTTGCAGATACCAACCATCGGCATTGGAGCTGGGCCTTTCTGCAGTGGCCAGgtttataagaaacttaacgttcttcgctcggaaacttacaaaggaa---aaaacgcttctttttttttccattgcag--------------------------

upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ24767 (Selaginella moellendorffii), 5'ss of exon 4
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt--ctctatctctctactaagataaatacccgtgttttttgtatgttttcttttgttgctaagaaaaaatatgaaaaccaagttggtctattt
 ||||| || ||| | ||  | || ||||||||||| |  || ||  || | |  || || ||||| ||||| |||||||| |||||||||||||| |||||| || |    ||  |  |   |     |  || |  |   |           |||| ||   ||||                                  
GGTTCTCGAGTGTATACCATCGCCAGTGGCTGCTGCCATCACTTCGTCCTTGCAGATACCAACCATCGGCATTGGAGCTGGGCCTTTCTGCAGTGGCCAGgtttataagaaacttaacgttcgtcgctcggaaacttacaaaggaagaaacgcttttttttccattgcag--------------------------------

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|34319717|gb|CF372471.1|CF372471
EST:     TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAG                         GTGCTAGTTTANCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
genomic: TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
EST: gi|110428509|gb|EC994983.1|EC994983
EST:     TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAG                         GTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
genomic: TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
EST: gi|110685873|gb|EE062975.1|EE062975
EST:     TTCGAATCCCC-CCATTGGCATAAGAGCTGGACCTTTCTGCAGTGGACAG                         GTGCTAGTTTACCATGATCTGCTGGGAATGATGCACCACCCAC
genomic: TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCAC
EST: gi|110685865|gb|EE062960.1|EE062960
EST:     TTCGAATCCC-ACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAG                         GTGCTAGTTTACCATGATCTGCTGGGGATGATGCA
genomic: TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAATGATGCA
EST: gi|110684865|gb|EE062628.1|EE062628
EST:     TCGAATCCC-ACCATTGGCATAGGAGCTGGAACCTT-CTGCAGTGGACAG                         GTGCTAGTTTACCATGATCTGCTGGGAATGAATGCA-CACCCACATCATGC
genomic: TCGAATCCCCACCATTGGCATAGGAGCTGGA-CCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAATGA-TGCAACACCCACATCATGC
EST: gi|110428428|gb|EC994900.1|EC994900
EST:     GCTGGACCTTTCTGCAGTGGACAG                         GTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
genomic: GCTGGACCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
EST: gi|110704726|gb|EE081728.1|EE081728
EST:     TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAG                         GTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
genomic: TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
EST: gi|110685210|gb|EE063373.1|EE063373
EST:     TTCGAATCCC-ACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAG                         GTGCTAGTTTACCATGATCTGCTGGGAAATGATGCA-C-CCCACATCATGC
genomic: TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAA-TGATGCAACACCCACATCATGC
EST: gi|110704743|gb|EE081769.1|EE081769
EST:     TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAG                         GTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
genomic: TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
EST: gi|71875196|gb|DT024251.1|DT024251
EST:     TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAG                         GTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
genomic: TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
EST: gi|110373622|gb|EC937874.1|EC937874
EST:     TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAG                         GTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT
genomic: TTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattatt ... tatactgcagGTGCTAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgattattctctatctctctactaagataaatacccgtgttttttgtatgttttcttttgttgctaagaaaaaatatgaaaaccaagttggtctattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaaa