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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttaataactgctctcaatgacttgaggttccttttgaaaatttcatttctttggagttagctacttatgggggcctatatctcacagtttcagttatttttttaatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGTGGGGATCCTCCCACATGTGGACAACTTTGCTCATATTGGAGGATTTGTTT

Basic information

species Vitis vinifera
transcript Vv06s0004g04890.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g05430.1 (Oryza sativa), 3'ss of exon 1
gtacttaataactgctctcaatgacttgaggttccttttgaaaatttcatttctttggagttagctacttatgggggcctatatctcacagtttcagttatttttttaatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGTGGGGATCCTCCCACATGTGGACAACTTTGCTCATATTGGAGGATTTGTTT
                              |||   | | | |  |  ||   |||    |   | | |  |   |   |   | |  |   ||   || || ||| |     ||||||||||||||||| |||||  |  | |||||  |  ||||  | || || ||||| || |||||||| ||||||||||||||| |||||||||||   |
------------------------------gtttgatctcaga--tctatgcatttattttacacaaatcctactgcatttcttgttgctaattgcattcttgtttaataatccagTTTGCAGCATTATTAACTCTAGTCATAATCATTCTCATCAACTTGGCTGTTGGGATTCTTCCACATGTTGACAACTTTGCTCATCTTGGAGGATTTACAT

upper sequence: Vv06s0004g04890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G100889_T01 (Zea mays), 3'ss of exon 3
gtacttaataactgctctcaatgacttgaggttccttttgaaaatttcatttctttggagttagctacttatgggggcctatatctcacagtttcagttatttttttaatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGTGGGGATCCTCCCACATGTGGACAACTTTGCTCATATTGGAGGATTTGTTT
                           |  | | ||     | ||    | | ||   |      | | |||      | || | ||  | | |    |  |||   ||    |||||||||||| | ||||||||  || | |||||  |  ||||  |||| || |||||||| |||||||| |||||||| |||||  ||||||||||| | |
---------------------------gtcgattctaaaatatatgcagtattttcacaaaacattccatat-----tccatttttctaattctattcttgtttcgaaaaaaacagTTTGCAGCACTCTTGACTCTAGTTATGATCATTCTCATCAACTTAGCTGTTGGGATCCTTCCACATGTTGACAACTTCGCTCACCTTGGAGGATTTATGT

upper sequence: Vv06s0004g04890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G04230.1 (Glycine max), 3'ss of exon 3
-----gtacttaataactgctctcaatg-acttgaggttccttttgaaaatttcatttctttggagttagctacttatgggggcctatatctcacagtttcagttatttttttaatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGTGGGGATCCTCCCACATGTGGACAACTTTGCTCATATTGGAGGATTTGTTT
         | || || ||   |||||  | | | | || |||   || |  | ||    |  |  || |      |  |     ||| |||      ||   |  || | ||  |   ||||||||||| ||| ||||||| ||  ||||| |  || ||||| |||| || || || || |||||||||||||| ||||||||||||||||||||||| |
gtgaatggatcaaaaaatgtgttcaattcaatagtgcttgcttcgtaataaatgatccgctctgcctttgtg--caacagacatttatttcttttccattttatgtttgtattgttttgcagTTTGCAGCGTTACTGACTCTTATAGTCATCGTTGTAATCAATTTAGCTGTTGGAATTCTTCCACATGTGGACAATTTTGCTCATATTGGAGGATTTGTCT

upper sequence: Vv06s0004g04890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G41170.1 (Glycine max), 3'ss of exon 3
----gt-acttaataactgctctcaatg-acttgaggttccttttgaaaatttcatttctttggagttagctacttatgggggcctatatctcacagtttcagttatttttttaatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGTGGGGATCCTCCCACATGTGGACAACTTTGCTCATATTGGAGGATTTGTTT
    || | | || || |    || ||| | | | |  | |||   || |  | ||    |  |  || |      |  |     ||| | |      |||  |  || | ||  |   ||||||||||| ||||||||||| ||  ||||| |  || ||||| ||||  | ||  | || |||||||||||||| ||||||||||||||||||||||| |
gtaagtgaatcaacaaatctgttccatgcaatggtgcctgcttcctaataaatgatccgctctgcctttgtg--caacagacatttattttttttccattctatgtttgtattgttttgcagTTTGCAGCGTTATTGACTCTTATAGTCATCGTTGTAATCAATTTAGCCATTGGAGTTCTTCCACATGTGGACAATTTTGCTCATATTGGAGGATTTGTCT

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|110364763|gb|EC928246.1|EC928246
EST:     ATCACAAAATTTGGACAATATATGCAAAATAAG                         TTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGT
genomic: ATCAC-AAA-TTGGACAATATATGC-AAATAAGgtacttaata ... taatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGT
EST: gi|110702261|gb|EE080769.1|EE080769
EST:     GAGGGATGCTTTCGGAACTCATCACAAATTGGACAATATATGCAAATAAG                         TTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGTG
genomic: GAGGGATGCTTTCAGAACTCATCACAAATTGGACAATATATGCAAATAAGgtacttaata ... taatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGTG
EST: gi|110382751|gb|EC947072.1|EC947072
EST:     GAGGGATGCTTTCAGAACTCATCACAAATTGGACAATATATGCAAATAAG                         TTTGCAGCATTATTGACTCTCATTCTCATCATCATAAGTCA-TCTAACAGT
genomic: GAGGGATGCTTTCAGAACTCATCACAAATTGGACAATATATGCAAATAAGgtacttaata ... taatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATA-GTCAATCTAGCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctacttatgggggcctatatctcacagtttcagttatttttttaatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGTGGGGATCCTCCCACATGTGGACAACTTTGCTCATATTGGAGGATTTGTTT
                                          ttttaat  putative branch site (score: 3)
                                    ttattttttt  CT-rich tract
                            agtttcagttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttaataactgctctcaatgacttgaggttccttttgaaaatttcatttctttggagttagctacttatgggggcctatatctcacagtttcagttatttttttaatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGTGGGGATCCTCCCACATGTGGACAACTTTGCTCATATTGGAGGATTTGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT