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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

Basic information

species Vitis vinifera
transcript Vv01s0026g00990.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 3
ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgactaattgct--ttatt--tttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
  |   |||   |||||| | ||| |  |  ||  ||   | |      | | | || || | ||| || |  ||| |  | | | |  | |  | || || || ||||||||||||| || || ||||||||||| || || ||||| ||||| || ||||| ||||||||  | |||||||| || ||||| ||||||
--tggttgtgcctgctagcagtttgtagcaatt--cacccttaatgaaatgtttcagttttagtaagtgatggttactaatgtttccccactctttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCCGGAAGCACTTACCGTACCAGGGATGAGATCTCAGGTGTAAGACAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
-----ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
     | ||||  | |  |    |      ||  |||||  |||     | || |   | |   || || ||  |     || | |||    |  |    ||||||| ||||| |||||||| || || ||||| || ||||| ||||| ||||| || ||||||||||| ||| | ||||||||  ||||  | || |||
aggacccttaaactagacgaggcttgaca-tcggttttgtgattccagactttcttcttaaagatg-ctgatcaccacggttctattc---gttttatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G140150_T01 (Zea mays), 3'ss of exon 3
ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagat--tgactaattgctttatttttcttctaaatgctg-gtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
 |   | ||  |  || ||    | | | | ||||  |  | || |||| || | |  |  ||| |||| |  ||| |   |    |  | ||  || |  || | ||||| ||||| || || ||||||||||| ||||| ||||| ||||| || ||||| ||||| ||  | ||||||||||| ||||| || |||
gtgataagtgataacttgttcactttgtttgttggt-tcataattatttaatttcatgtgctgaataatgg--ttactaaaccctcatgttctatgtatctagGTCCTTGAGATGGATACCTACAGGTACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
---------------------ctttaatgttgttgct-agtaatttctct--cttttggcattg---tcatcattttatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                      | || |  | ||  | |  ||||| | |  ||||| | | ||      | ||| | ||| | |||   |||||| ||| | | ||||   |||  |  ||| |||||||||||||||||||| || || |||||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatatta--taattgatttctctatctt---aattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
-ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattt--tatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
  |||||  | | ||  | |  | |   | |  |   ||| |||   |||  | ||| |||||   | |||| ||| | | |||| |  ||  |  ||| ||||||||||||||||||||||| || |||||||| ||||| |||||||||| ||| ||||| ||||||||||||||||| ||||||||||||||||||
attttaacatagctgtcatttgtgtagttttgattaaattatcaaagtttattctgttagatt---tgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgact-aattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
 ||||   | | ||  | |  | |   | |  | | ||| ||||  |||  | |  | | || |  |||| ||| | | |||| |  ||  |  ||| ||||||||||||||||||||||| || |||||||| ||||| |||||||||||||| ||||| ||||| ||||||||||| ||||||||||||||||||
-tttatcatagctgtcatttgtgtagttttgattgaattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
------------------ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgacta-attgc--tttatttttct-tctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                   |||  |  |  |  |  | |  | | | ||| |   ||   |    ||  | |    |    || ||| |  || |||| ||| ||| |||  |  ||| |||||||| || |||||||| || || |||||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||||||||| ||||||
gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
ctttaatgttgttgctagtaatttc--tctcttttggcattgtcatcattttatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
| |  | || || |||     || |  | | ||||    |  | ||  |||  | | | || || ||         |  | | ||    | ||  | | ||||||||||| |||||||| || |||||||| ||||||||||||||||||||||||||||| |||||||| || |||||||| ||||||||||| |||
catataagtagtagctttggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatc--gtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G24180.1 (Arabidopsis thaliana), 3'ss of exon 3
ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgactaattgctttatttttcttctaaatgctggtgtt----cagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
 | | |  |   |   |     ||  |  || | | ||| | || ||    | |     |  ||| |   | |      | |   | |||   | ||    ||||| ||||| ||||||||||| || ||||| |||||||| |||||||| || || ||||| |||||||| |||||||| || ||||| |||||||||
ttgtgaattcaatcacatagcgttgacatttatcgtatttttataatccattct----ctacctagtgattatgaccaacataccattgccattatttgcgcagATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S201_84V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------ctttaatgttgttgctagtaatttctctcttttggcattgtcatcat--tttatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                                                               |||| |    |||||     || |    ||  | || |    || |     |  ||   |||  |   | |||| | |   || ||  | ||||  |  || || | || ||||| || || || || ||||||||||| |||||||| || || ||||||||||| || ||||||||||| ||||||||  |||||
gtaagtgatgctgttgttttcctaaccagcacatggatactttaccttcttctaatcatggggtttactccatttgctgtgtgttgcagctttacgtcagttatgtcgtaaccgagatgcttttgcttgggttctttttctgaattatattttctggcatggagGTTTTGGAGATGGATACGTACAGATATCATGGTCACTCTATGTCTGACCCAGGCAGCACCTACCGAACCCGTGATGAGATCTCTGGTGTACGACAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S56_222V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------ctttaatgttgttgctagtaat-ttctctcttttggcattgtcatcattttatgtgagattgactaattgctttattttt------cttctaaatgctggtgttcagA-------TTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                             | | ||   |||| ||  | |||||     |    |        | ||| |||   |   |||    |||| |||||       |||| || | || | |   ||       || | || ||||||||||||||||| ||||||||||| |||||||| || || |||||||| || || ||||| ||||| || |||||  |||||
gtaagttctgctggaaaatttgaaaatcattacgtcaatgctcgtcttattctccaggcttttctcaatggagtgttacgtgccgtcagctacgcactttgtttttgagtgatttctgaaaggtgttttgtggaatgaagGTTTTGGAGATGGACACTTATAGGTATCATGGTCACTCTATGTCTGACCCAGGCAGCACCTATCGAACTCGTGACGAGATCTCCGGTGTCCGACAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ36226 (Selaginella moellendorffii), 3'ss of exon 3
ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgactaattgctttatttttcttctaa-atgctggtgtt-cagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                                       || | | | |   ||     |  ||  | |||||| |  ||       |||     ||| ||| |  | |||||||| |||||| | || ||||| ||||||||||||||||| ||||| || || || ||| | || |||||||| || |||||||||
---------------------------------------gtaagcttatctagtttttatatcttttggctttactcctcacgggggatgggaacgttacagGTGTTGGAAATGGATACTTATCGTTATCATGGGCACTCCATGTCTGATCCCGGGAGTACATATCGGACAAGGGAAGAGATTTCCGGCGTGAGACAG

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|110417777|gb|EC983859.1|EC983859
EST:     AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
genomic: AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
EST: gi|27585723|gb|CB008418.1|CB008418
EST:     AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
genomic: AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
EST: gi|110360358|gb|EC923399.1|EC923399
EST:     AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
genomic: AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
EST: gi|110383536|gb|EC947914.1|EC947914
EST:     AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
genomic: AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
EST: gi|27583148|gb|CB005843.1|CB005843
EST:     AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
genomic: AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
EST: gi|30298455|gb|CB975249.1|CB975249
EST:     AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGCACCATGGTCACTCCATGTCTGATCCT
genomic: AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
EST: gi|110384826|gb|EC949291.1|EC949291
EST:     AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
genomic: AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
EST: gi|110703998|gb|EE081422.1|EE081422
EST:     CATGCTTTATAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
genomic: CATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
EST: gi|110415427|gb|EC981335.1|EC981335
EST:     AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
genomic: AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
EST: gi|110423195|gb|EC989535.1|EC989535
EST:     AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
genomic: AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
EST: gi|32245966|gb|CD711785.1|CD711785
EST:     AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT                         ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT
genomic: AACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac ... tggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG
                                   ttctaaa  putative branch site (score: 2)
                         tttatttttcttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - -tgttgct
- - - - - - - - - - - -tctctct
- - - - - - - - - - - - - - - - - -cattgtc