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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG

Basic information

species Vitis vinifera
transcript Vv00s0181g00220.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
                      || |||   ||    ||  |     ||  ||| ||| |  || | ||   ||   | |  | |||       || ||   | |   ||| |||||||| ||||||||||||||  | || ||||| |||||| |||||||||||||||| || |||||  |||| ||||||| | | ||   |  |||
--------------------gtatgattccatatactttactgatcttgtgtaactgt-tacatgtcttaacatatagatcttaaatt------ataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
                    |  ||   | | | || || || ||     |    |   ||      || | ||| |  | || || |  |    |  | | | |  |||| ||||| |||||||| || |||||  | || ||||| |||||| |||| || ||||||||||| |||||  |||||||||||| ||| |||  |  |||
------------------gtatgtttgcaatgagttattgttttactcatactgctagatg-----atttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 5
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
         | |   ||| || | | ||  ||   || ||  ||  |   |  | |   ||||| | || | ||     | |  || |     |||  | | |||   ||| ||||||||||||||||| |||||  |||| ||||| |||||| |||| || ||||||||||| |||||  |||||||||||| ||| |||     |||
--------gtatgt-gtgacacactgttgatttactcattagatgaaacaaagattacctgtattt-ttagaatttgcatcgccaagcatgctgattttgtatttattagTGTACAAGAAGCACTACCCACCTGCGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCCAGTGG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AC202073.4_FGT001 (Zea mays), 3'ss of exon 4
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
                        |||  |||| ||  | | || |     | ||    | || |   | || |  |     |||||  |  |  | | | ||||   ||| || |||||||| || ||||||||| | || ||||| || ||| |||| || |||||||| || ||||| |||||||||||||| || ||   |  |||
-----------------------gtat-gtttatttagtgtgatgtcattgttaaataatctaacatataggctt-taaacatgaatacgttaactaactcttttgt-agTGTATAAGAAGCATTATCCTCCTGCACTAAAGGATGAGGTATGGAGATTAGAAAAGATTGGAAAGGATGGTTCATTCCACAAGAGATTAAACTCAAGTGG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
                              | | | |     || |||   |  |  ||| |  |   | |    ||           |  ||  |||||| | |   ||| |||||||||||||| || ||| || |||| ||||| || ||| | ||||| || || || || |||||||||||||| |||||| |||| ||| ||||
-----------------------------gtaagtcccaaaaatgtatctgtgtac-tgtattcccacttgacatatatctaaactatttcaatttcatttatct---agTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G010471_T01 (Zea mays), 3'ss of exon 1
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatg-gtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
                                  |   |   | | ||| ||   ||||  | | |  |    |||    |    || ||     |   |  |||  | ||| |||||||||||||| || ||| || |||| ||||| || ||| | ||||| || || || || |||||||||||||| |||||| |||| ||| ||||
---------------------------------gtaagtcccaaaaatgtatttgtgtgc-tgtattctcacttgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 5
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaat-gtgtgtatctgttgggat----gatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
         | |   |||  | ||| ||  ||   || ||  ||  || || | ||   |||||| | || | |         || |  |   ||   |||  | | |||   ||| ||||| || |||||||| ||  |  |||| ||||| |||||| |||| || ||||||||||| |||||  |||||||||||| ||| |||     |||
--------gtatgt-gtgatacattgttgatttactcattagatg-atacaaagattacgtgtattttttagaacttgcatcagttgcaagcatgct-gattctgtatttattagTGTACAAAAAACACTACCCACCCACGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCTAGTGG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 3
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
                 || |  | || | || ||| | ||| |               | ||||| |   ||  || || || |   |||||  ||| ||   ||  |||||||||||| |||||||| ||||| ||||||||||| || ||| || |||||||||||||||| ||||||||||| ||||| ||| | |||||||||||
-----------------gtaagttcataacttccttatatttgt---------------tatatctttctagagaattgttgtaa---tgaaacttcaattgaatcgtagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 4
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
                 || |  | || | || ||| | ||| |               | ||||| |   ||  || || || |   |||||  ||| ||   |   |||||||||||| |||||||| ||||| ||||||||||| || ||| || ||||||||||||| || ||||||||||| ||||| ||| | |||||||||||
-----------------gtaagttcataacttccttatatttgt---------------tatatctttctagagaattgttgtaa---tgaaacttcaattgaattatagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGTAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgt-tgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
                                           ||  | ||||||  |   | | | | |   ||  |  |  || |  ||| |  |    ||  |  |||||||||||||||||||||| ||||| ||||||||||| || ||| || |||||||||||||||| ||||| || || ||||| ||| | |||||||| ||
------------------------------------------gtaagtacataaacttcattgtttatgttctatccttcttctgtaa-tgatacttatacttgattgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S336_7V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------gtgagttgatgttcagtgtcaaattattatttacttctttttatata-tgcataaatg-----tgtgtatctgttgggatgatggtggtgaatctgaaagatc---atttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAAT-AAAGCTGG
                                          |||||  | | |  |   || |||   ||   ||| |||||   | |  ||||| |     ||  ||| | |   ||||   ||  |||||||     |        |||    |||| |||||||||||||| || ||||| |||||||| || || ||||| ||||| |||||||| || || ||  | || |||||| |  | ||| ||| |   
gtacgttgactgttttgaaccttgggtcatcttacgctataagagtttgtctgcgttcctaatttacagttagtttcgttttaggcagttaataaaagcagtttgaatatttatctagatggaagtattgaatcttttctacttgggaatttcgtgcagTGTACAAGAAGCACTATCCACCTGCCTTGAATGACGAGGTATGGCGCTTGGACAAGATTGGGAAGGACGGAGCCTTTCACAAGCGCCTCAATCAAAACCA-

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S84_168V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgagttgatgttcagtgtca-aattattatttacttctttttatat-atgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
|    || | | ||  ||  | || ||  |   |    |    |||| | | ||  ||  || | | | ||   |  || || ||   ||  |           ||   |||| ||||||||||||||||| ||| | ||||||||||| || ||||||||||| || |||||||| || ||  | || |||||| |  | ||| |  || |
gcctttttacggtccctggaagaagtacgaaggatcagtggaaatattaggaatggatacgtttctgt-ttctaagaatcgttgtcggtcaca-----------ttctgcagTTTACAAGAAGCACTACCCGCCTTCCTTGAATGATGAGGTCTGGCGATTGGACAAAATTGGCAAGGACGGTGCTTTTCACAAGCGTCTCAATCAGTCTCG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S98_167V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
 ||   || ||  ||        || |    |   |    | ||  |   |  ||      ||||| |     | ||  | ||   |      | |||  || | |  ||| |||||||||||||| || ||||| || ||||| || |||||||||||||| |||||||| ||||| ||  | ||||||||  |  | ||| ||||  |
-tgccctg-tgcacatccattcgttctgtgctgaatgccgtgattaacagaagaaaaatcatatctctatatctaataattgttgtt------ggtcaccttgtac--agTCTACAAGAAGCACTATCCGCCTGCTTTAAATGACGAGGTTTGGCGATTGGACAAGATTGGAAAAGACGGTGCTTTCCACAAACGTCTAAATCAAGCAAG

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatga-tggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
         ||||| ||| |||| | ||    |       | |   | ||||   |   || ||  | ||  |  | |    ||     |        |  |||    |||| ||||| ||||||||||| ||||| |||||||| || || ||||| ||||| |||||||| ||||||||  | ||||||||| |  | ||| ||||   
--------ttgttcggtgccaaagtttttgaaaaaaagaatcaggca-gcatgg-tacttg-attggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA

upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S34_132V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgagttgatgttcagtgtcaaattattatttacttctttttatat--atgcataaatg-tgtgtatctgttgggatgatggtggtgaatctgaaagatcattttttt-cccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
                || || |||   |  |  |  |    | |   | | |   ||| ||     |           |  |  ||| | |    | | |||  | |   |||| |||||||||||||| || || || |||||||| || |||||||||||||| |||||||| ||||| ||  | ||||||||| |  | ||| |||||  
--------------tctgccagatttccaagttgtgatcagaagaagaaagaagggatggtgaaagcccaacatatctgtatttttgattattgttgttgattactctgttcagTTTACAAGAAGCACTATCCACCAGCCTTGAATGACGAGGTTTGGCGATTGGACAAGATTGGGAAAGACGGTGCTTTCCACAAGCGTCTAAATCAAGCTCA

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|33402821|gb|CF208448.1|CF208448
EST:     TCGTGAAGC-AAAACAGATGCCTTCACTGTTAAGGATCAGATAGGGGAAT                         TATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGG
genomic: TCGTGAAGCAAAAACAGATGCCTTCACTGTTAAGGATCACAGAGGGGAATgtgagttgat ... tttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
                                        tcatttttttccc  CT-rich tract
                                   aaagatcattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG