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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttatcagaacctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatctttactgtcttccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA

Basic information

species Vitis vinifera
transcript Vv13s0019g05390.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os09g39690.1 (Oryza sativa), 3'ss of exon 6
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttatcagaacctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatctttactgtcttccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA
          | ||          ||| | ||||  ||      |  |   |      |   |    | |||    |   ||    |   | |      |    |||| ||   | | | | |   |  ||  | ||   |        ||||||||||||||||||||| ||||||||||| || ||||||||||||||  | ||||| || |||||  ||||||| || || ||  ||||||| ||||||
----------gtttgaactcatgcttttcttctgaaataatgaataataggtccatgtagttt----gttcttctctaatacagtataacagtacta-atgatggtttgttttgcctctttgttgggggttggggtgttgactttctatcagATGTGGGCACATGTGCACATGTTCAAAATGCGCGAATGAGTTGGTTCGAAGCGGAGGGAAATGCCCGCTGTGCCGTGCACCCATAATTGAGGTGATCCGA

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g57750.2 (Oryza sativa), 3'ss of exon 5
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttatcagaacctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatctttactgtcttccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA
                                           |    ||   | |  ||| |    |||  |  |||    |||    |||| ||   |  |  ||| |  |   | |  ||  |     || ||     |   ||  |||||| ||||||||||| ||||| |||||||||||||| ||| |  ||||  |||| || || |||||| | |||||||| ||||| |  |||||  | || 
------------------------------------------gtcagcttcacagctaaacatgtctgat--actttgatgttac----taatctc---taaccttttttgtctgatgtacttg-taaaacccatttggtgatggtg-acagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G006965_T01 (Zea mays), 3'ss of exon 6
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttatcagaacctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatctttactgtcttccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA
                      |||  | | |   || |    | | || |||||  ||    |  |  |  |      | |||  | ||  |     || |||||        | | | |||  ||| |     |||           |||||||||||||||||||||||| || ||||| ||||| || |||||||| |||||||| || ||||| |||||||| || || ||  | ||||||||||||
---------------------gtttggctcgcattgaccacattctattatttattgga----cgagtgttgaatcatagtctatatgttggta----gtagctgtgaa-----cctgttttttgtgtttattactgat----------cagATGTGGGCACATGTGCACTTGCTCGAAATGCGCAAACGAATTGGTTCGAGGTGGAGGGAAATGCCCGTTGTGCCGCGCACCCATAATCGAGGTCATCCGA

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G081965_T01 (Zea mays), 3'ss of exon 6
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttatcagaacctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttcc-ccttatctttactgtctt----ccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA
                                                         |   ||||       || |  ||  | |||| |     |  | || ||| | |    | | || | || ||  ||    |  | |    |  ||| |||| |||||||||||||| ||||| || ||||||||||||||| |||| ||  | || || ||||||||  | ||||| || || || || |||||  |||| 
------------------------------------------------------gtgggtactccacatgacatttcagg--ttccttgtg--cacaagctggtgtatgtgatgcgtgatttgtaatgctttaaacctttcgggtgatgatg-gcagGTGTGGGCACATGTGTACTTGCTCGAAATGTGCAAATGAGCTGGTGCGCAGCGGCGGCAAGTGCCCGCTCTGCCGGGCTCCCATCGTGGAGGTGGTCCGC

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 8
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttat---cagaac------ctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatct--ttactgtcttccgttgaaaaaaaatg---tgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA
                  || ||| | |    |   || |||  ||| | || ||   || ||       | |     | |||   || |       || ||   || |   | ||     | ||  | |  || ||  ||| ||   ||    |||    |||||||||||||||||||||||||||||||||||||| ||||||||  |||||||||| || || || || || |||||||| || |||||||||||  |||||
------------------gtacttatacatgataaaatatataatttgtgttgatgaacaaaaaatacaaccctacattttatgcaggtatctgtagtttatactgtttacttattctgaacactggttttgtttcttcctttcggcaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTGTTGAGGTGGTCCGA

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 9
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttatcagaacctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatctttactgtcttccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA
                  ||  || | |  | |   || |||  ||| | || || |  |          |||  ||   |    |  |   |||  | || |||     |    || | | | |  |  |||       ||     |||||||||||||||||||||||||||||||||||||| ||||||||  |||||||||| || || || || || |||||||| || ||| |||||||  |||||
------------------gtatttatacattatactatatataatttgtgttgatgaacaaaatacaaccctacattataatatgcact--gtttactttttctgaacactggttttgtttcttcctttctccaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTCTTGAGGTGGTCCGA

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G04460.3 (Arabidopsis thaliana), 3'ss of exon 7
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttatcagaacctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatctttactgtcttccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA
                                                                  | | ||| ||     ||    |  ||       ||  ||| ||||   || |    |       ||| || |||       | |||||| || |||||||| ||||| |||||||||||||||||| | ||  |    |||||||| || ||  | ||  |||| |||||  | ||||| ||||||
------------------------------------------------------------------gtaactaact-aactctttgctcaaaaaaaaaattattgtctcttaaactcaaaactgaacaaatcctttaaaat------tacagATGCGGACACATGTGTACTTGCTCAAAATGTGCAAATGAGCTTGTAAGAAACGGAGGAAAATGTCCGCTTTGTAGAGCACCGATCATCGAGGTAATCCGA

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|33404834|gb|CF210461.1|CF210461
EST:     GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAG                         ATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
genomic: GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAGgtatatgcct ... aaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
EST: gi|110362870|gb|EC926428.1|EC926428
EST:     GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAG                         ATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
genomic: GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAGgtatatgcct ... aaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
EST: gi|110402602|gb|EC960544.1|EC960544
EST:     GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAG                         ATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
genomic: GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAGgtatatgcct ... aaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
EST: gi|30302439|gb|CB979233.1|CB979233
EST:     GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAG                         ATGTGGGCACATGTGCACTTGTT
genomic: GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAGgtatatgcct ... aaatgtgcagATGTGGGCACATGTGCACTTGTT
EST: gi|110697361|gb|EE074284.1|EE074284
EST:     GGAACTTGTTGTGTTTGTTGTGATAACCACATCGACTCTCTATTGTACAG                         ATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAATTGGTTCGTGG
genomic: GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAGgtatatgcct ... aaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
EST: gi|110722021|gb|EE097887.1|EE097887
EST:     GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAG                         ATGTGGGCACATGTGCACTTGTTCAAA-TGTGCAAATGA-TTGGGTTC-TG
genomic: GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAGgtatatgcct ... aaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGG-TTCGTG
EST: gi|30297155|gb|CB973949.1|CB973949
EST:     GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAG                         ATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
genomic: GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAGgtatatgcct ... aaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
EST: gi|110396940|gb|EC962647.1|EC962647
EST:     GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAG                         ATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
genomic: GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAGgtatatgcct ... aaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
EST: gi|34362695|gb|CF404280.1|CF404280
EST:     GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAG                         ATGTGGGCACATGTGCACTTGTTCAANCTGAGCCAATGAGTTGGTTCGTGG
genomic: GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAGgtatatgcct ... aaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
EST: gi|110405556|gb|EC971098.1|EC971098
EST:     GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTTTTTATTGTACAG                         ATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG
genomic: GGAACTTGTTGTGTTTGTTGTGATAGCCACATCGACTCTCTATTGTACAGgtatatgcct ... aaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgctgtttcttccccttatctttactgtcttccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA
                                     ttgaaaaaaaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttatcagaacctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatctttactgtcttccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA