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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcctcttcaatctgtatatttattacaaagccagtttgtacatgattcagtaatcatcagtactcatctgtatggaataagtgtatcttttcc...

Basic information

species Vitis vinifera
transcript Vv02s0025g03530.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgt-----agttagcctcttcaatctgtatatttattacaaagc------cagtttgtacatgattc--------agtaatcatcagtact-----catctgtatggaataagtgtatcttttcc-----------------------------------------------------
|||||||||||| ||||  | || ||||| ||||||||||| || || |||||||| || |||||||||||||||||||||||     || |  |  |||    ||   | | |||| |    |      |||| ||  | || |          ||||| ||  |  | |     |||  |||  | |  | | ||| | ||||                                                     
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagcttactcctttgcacttcttttgtatttctgtacactttgcagtgtggtcttggtgtcaagtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 12
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgta-gttagcctcttcaatctgtatatttattacaaagc----cagtttgta-catgattc---------------agtaatcatcagtact-----catctgtatggaataagtgtatcttttcc-----------------------------------------------------
|| ||||||||| ||||  | || ||||| ||||||||||| || || |||||||| || ||||||||||||| |||||||||  |||||| |  ||  | || |  | | ||  |   |    ||||||| |   || |                 ||||| |   || | |     |||  |||  | |  | ||||| | ||||                                                     
GTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGGgtttgttagcttactcc-tttgcacttcttttgtatttctgtacagtttgcagtgtggtcattggtgtcaagtagaagtaaacgcaaggagtttggacatgggtactgtagtaatgtatatcttccatgttctataggaagaattttgaaccagttttggaattggtatttgtatacag

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 11
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcct------cttcaatctgtatatttattacaaagccagtttgtacatgattcagt-aatcatcagtactcatctg-------tatggaataagtgtatcttttcc-----------------------------------------------
|| ||||| ||||| ||| | || ||||| ||||||||||| || || |||||||| || ||||| ||||| |||||||||||   |   ||      |||  |  |   | | |||| |   ||     ||| | |    |||  | |  | | ||   || ||       || || || ||| ||| | |  |                                               
GTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGGgtttgtgatctgctttcctttgacttcgttttgtattcctgtgcactgctgtgcctctgacagccagtagttaatatgaatatgggctatctacggtattagtttatttatagcttttgctagaagttttaaccagaatttggcttcatgcgagtccacag

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 11
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcct------cttcaatctgtatatttattacaaagc-cagtttgt-acatgattcagtaatcatcagtact-catctgtatggaataagtgtatcttttcc------------------------------------------
|| ||| | ||||||||| | || ||||| ||||||||||| || || |||||||| || |||||  |||| |||||||||||   |   ||      |||  |  |   | | |||| |   || | |    | |||      ||| |  |||| ||     ||| |  || |  ||| ||| | |                                             
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttctgtgcactgccactgacagccacaagttaatatcaatatggtctctctgcggtagtagtttatttctagtttttgctggaagttttaatcagaattttgtttatgtctacag

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA08G01750.2 (Glycine max), 5'ss of exon 11
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcctcttca--atctgtatatttattacaaagccagtttgtacatgat-tcagtaatcatcagtac-tcatctgtatggaataagtgtatcttttcc
||||||||||||||||| ||||| ||||| ||||||||||||||||| ||||| |||||||||||||| ||||||||||||||   |  ||| || |  |  |||  |     |     | || || |    |||  |  | | |  ||| |   | || |||     || |   |   ||    
GTCAGGCTGAAGAGATATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGGTTATGTGCTTTACCAGCATTTTGGgtgagtgacctttttactacttgtgcacgatgtttgtggtcacttagcctctgacatttggattgttcactgtattatttgt-caacatcaaaatggtttc---

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 12
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcctcttca--atctgtatatttattacaaagccagtttgtacatgat-tcagtaatcatcagtac-tcatctgtatggaataagtgtatcttttcc
|||||||||||||| || ||||| ||||| ||||||||||||||||| ||||| || || |||||||| ||||||||||||||   | |||| || |  |  | |  ||    |     | || || |    |||  |  | | |  ||| |   | || |||    |  ||     | |     
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcctttttactacttctgcatgatgtttgtggtcacttagcctctgacatttggattgttcactgtattatttgtcaacatcaaaatggtgtc----

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 12
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcctcttcaatctgtatatttattacaaagccagtttgtacatgattcagtaatcatcagtactcatctgtatggaataagtgtatcttttcc
||  || |||||||||||||||| ||||| |||||||||||||| |||||||||||| | |||||  ||||||| || ||||||  ||      | |     |||||  ||| |      | |  |   ||| ||||  ||  ||      |  | |  ||   ||      || |     
GTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGGgtaactacatctattagcacatatat--atttcgtgcttaat--gagaatgtttcaaaaagtattgactgttgttttgattttatctacaaatttcag--

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|27580232|gb|CB002927.1|CB002927
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|22009546|gb|BQ794580.1|BQ794580
EST:     GTGCTGATGTAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|254917830|gb|GR903482.1|GR903482
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATAATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|110428549|gb|EC995024.1|EC995024
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATAATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|110725594|gb|EE102275.1|EE102275
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATAATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|32245737|gb|CD711556.1|CD711556
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATAATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|30130004|gb|CB915343.1|CB915343
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|22009504|gb|BQ794538.1|BQ794538
EST:     GTGCTGATGTAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|27586164|gb|CB008859.1|CB008859
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTCATATGATGAAGTTTCACTACAAAATGCTCTGGACATAATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|30297452|gb|CB974246.1|CB974246
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATAATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|32246359|gb|CD712178.1|CD712178
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATAATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|32247869|gb|CD713688.1|CD713688
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|30125117|gb|CB910456.1|CB910456
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|30322432|gb|CD005694.1|CD005694
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA
EST: gi|37187375|gb|CF606728.1|CF606728
EST:     GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG                         GTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATAATA
genomic: GTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcc ... tatatgtcagGTAGGCATTTTATATGATGAAGTTTCACTACAAAATGCTCTGGACATTATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcctcttcaatctgtatatttattacaaagccagtttgtacatgattcagtaatcatcagtactcatctgtatggaataagtgtatcttttcc

- - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaataa