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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAAGCACCAGGGCCTGGCTATACTTGTGGACCTGCGAAGATCGTTAAACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttcttgatgtagattacagagtattttggatacatttatgcacttcattcaacatcagtgacctagatggtactatgatttctcaaatttatag...

Basic information

species Vitis vinifera
transcript Vv14s0083g01160.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA05G00210.1 (Glycine max), 5'ss of exon 3
CTGAAAGCACCAGGGCCTGGCTATACTTGTGGACCTGCGAAGATCGTTAAACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttcttgatgtagattacagagtattttggatacatttatgcacttcattcaacatcagtgacctagatggtactatgatttctcaaatttatag
                                |      ||| || ||  | |||   | |   | |      |        ||  |  |||| ||   |  ||  ||     |  |     ||| |     ||| || | || ||  | |    ||| ||     | | |  |     ||| |     ||||       
-------------------------------AATGCAATAAGTTCATTTCAACTAAGTGTTGGTTTAGCTGGAACAACTAACGAAACTGTCAAACTGCCAAAAAAATTTACCCTCAAAGCACCAGGGC---CTGgttaaacttgtggccctg--ccaagattgtgaaaccaactaaatttattac----caaag------

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA17G08830.1 (Glycine max), 5'ss of exon 2
CTGAAAGCACCAGGGCCTGGCTATACTTGTGGACCTGCGAAGATCGTTAAACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttcttg--atgtagatt-acagagtattttggatacatttatgcacttcattcaacatcagtgacctagatggtactatgatttctcaaatttatag--
|| ||||||||||||||||| ||||| ||||| ||||| ||||| || ||||| |||| |||| | ||  ||||    ||||||  |||||| || || |||||||| ||||  |  |  ||| |||    || ||| ||| || |      ||| ||| | |    | | ||  |     || |  ||||| | || ||     
CTCAAAGCACCAGGGCCTGGTTATACCTGTGGCCCTGCCAAGATTGTGAAACCAACTAAATTTATTACTAAAGACAAGAGGAGAACCACTCAGGCATTAAgtaagttacttgcaaaatgcattgacatgaaatgttgaatatatatccatgtttctttctaaac---ttagctgaaaaac-ctttagtttct-agatgtactata
















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|30128146|gb|CB913485.1|CB913485
EST:     ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGA                         TGACATGGAATGTTACATGCACATATTCACAATTCCTGTCTCAGAAAACCC
genomic: ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttct ... tctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCC
EST: gi|110371120|gb|EC934895.1|EC934895
EST:     ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGA                         TGACATGGAATGTTACATGCACATATTCACAATTCCTGTCTCAGAAAACCC
genomic: ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttct ... tctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCC
EST: gi|110699176|gb|EE075944.1|EE075944
EST:     ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGA                         TGACATGGGATGTTACATGCACATATTCACAATTCCTGTCTCAGA
genomic: ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttct ... tctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGA
EST: gi|30137657|gb|CB922995.1|CB922995
EST:     ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGA                         TGACATGGAATGTTACATGCACATATTCACAATTCCTGTCTCAGAAAACCC
genomic: ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttct ... tctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCC
EST: gi|110724325|gb|EE100052.1|EE100052
EST:     ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGA                         TGACATGGAATGTTACATGCACATATTCACAATTCCTGTCTCNNNNNNNCC
genomic: ACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttct ... tctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAAAGCACCAGGGCCTGGCTATACTTGTGGACCTGCGAAGATCGTTAAACCTACTAGATTTGTGACACAAGATGGAAGGAGAGTCACTCAAGCTTTGAgtaagtttcttgatgtagattacagagtattttggatacatttatgcacttcattcaacatcagtgacctagatggtactatgatttctcaaatttatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT