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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacttttctacatgaattccctcatccattttcatttcttaatttttgatgccctctctaccttcctttatttcctttttttttttttttcttttttatcatcaccatgcattcatctctcctgtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACCGCAAGTATCGAAACGGGGATCGCCCCAACCGGGTCACCACTTCTGGCTA

Basic information

species Vitis vinifera
transcript Vv12s0035g02020.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g02160.1 (Oryza sativa), 3'ss of exon 1
gtacacttttctacatgaattccctcatccattttcattt--cttaatttttgatgccctctctaccttcctttatttcctttttttttttttttcttttttatcatcaccatgcattcatctctcctgtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACCGCAAGTATCGAAACGGGGATCGCCCCAACCGGGTCACCACTTCTGGCTA
                                |||||| |  |    | ||||||  | | |  |||||  ||   |  ||   ||||||     ||| ||  |  || || | |||  ||        |      ||| |||||  ||||||| || ||||| ||||||||||||||||| || ||||||||||| |||||||| ||||| |||||||| || ||  | || || ||
--------------------------------tttcatgtgaccccctctttgatttcatgtgaaccttt-ttgggtggctcacttttttcccaccttcttgttgctccccttacatggatgg-----atgcacccagCTCTGGCCTCAATTGGGGACAAGGAGTGGTTCTTCTATGTGCCAAGGGACCGCAAGTACCGAAACGGCGATCGGCCCAACCGAGTGACGCCATCGGGGTA

upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G123246_T01 (Zea mays), 3'ss of exon 1
gtacacttttctacatgaattccctcatccattttcatttcttaatttttgatgccctctctaccttcctttatttcctttttttttttttttcttttttatcat-caccatgcattcatctctcctgtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACCGCAAGTATCGAAACGGGGATCGCCCCAACCGGGTCACCACTTCTGGCTA
                                     || ||| | ||||  |||   |  |           |    |  |   |      |  |    |||   | |  | |||    |   |    | ||  ||| |||||| | || || || ||||| |||| |||||| ||||| |||||||||||||| || ||||| || |||||||||||||||||  | || |||||
-------------------------------------ttgctttacttttcgtgcatgcgatgatggtggcggtggtgtcatggatggacgatgctcaccatctcacgctcttcataatacgaacaaccacgaacagCTCTGGCTTCGATCGGGGACAAGGAGTGGTACTTCTACGTGCCGAGAGACCGCAAGTACCGCAACGGCGACCGCCCCAACCGGGTCACGCCGTCCGGCTA

upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G030325_T01 (Zea mays), 3'ss of exon 1
gtacacttttctacatgaattccctcatccattttcatttcttaatttttgatgccctctctaccttcctttatttcctttttttttttttttcttttttatcatcaccat-gcattcatctctcctgtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACCGCAAGTATCGAAACGGGGATCGCCCCAACCGGGTCACCACTTCTGGCTA
                               ||||  ||   |   | |   || |  ||      ||| |   |     |      |  |     | | ||  |||||   |||  | |   | ||| |      || |||||  | ||||| || ||||| |||| |||||| ||||| |||||||||||||| || ||||| || |||||||||||||| ||  | || |||||
-------------------------------ttttagttgtgtgcatgtgtctgtctactagctactccatggatatagatggacgctcatcgtcatctcatgctcaccgccgcacacgtacgtactgca------gCTCTGGCCTCCATTGGGGACAAGGAGTGGTACTTCTACGTGCCGAGAGACCGCAAGTACCGCAACGGCGACCGCCCCAACCGGGTGACGCCGTCGGGCTA

upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G813651_T01 (Zea mays), 3'ss of exon 1
gtacacttttctacatgaattccctcatccattttcatttcttaatttttgatgccctctctaccttcctttatttcctttttttttttttttcttttttatcatcaccatgcattcatctctcctgtatgagt--agCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACCGCAAGTATCGAAACGGGGATCGCCCCAACCGGGTCACCACTTCTGGCTA
                                   |    |  || |    |  |     |||    |||  | |||  | |  |    ||  ||     |       |      ||  |   | |||||| ||  |||  |||| || ||||| |||||||| |||| |||||| ||||| || ||||||||||| || ||||| ||  | ||||||||||| ||  | || |||||
----------------------------------ccgaccccgaactaaccagtcttgtgctagaagcctagaattcgatctaatcaagttgacta----agggctgacggatggtctgcatgcatgtatgcgtgcagCAATGGCCGCGATTGGGGAGAAGGAGTGGTACTTCTACGTGCCGAGGGACCGCAAGTACCGCAACGGCGACAGGCCCAACCGGGTGACGGCGTCGGGCTA

upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G147867_T01 (Zea mays), 3'ss of exon 1
gtacacttttctacatgaattccctcatccattttcatttcttaatttttgatgccctctctaccttcctttatttcctttttttttttttttcttttttatcatcaccatgcattcatctctcc--tgtatga----gtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACCGCAAGTATCGAAACGGGGATCGCCCCAACCGGGTCACCACTTCTGGCTA
|||  | |   |  |||   |  | ||| ||| |  |    |   | | || |       ||| | ||   |    |    | |   |   |  |   | || |   |  || || ||  |       | | |     | |||  |||| |  || || | |||||| ||||||||||| ||||| || ||||| ||||| || ||||| || ||||| |||||||| ||  | || || ||
gtaaccatcaattaatgg--tagcgcatgcatctggaagcttcgttctctgcttgatcagctagcctcgaattgaactgagtctcgatcgatcttggctaattaattcgttgtatacaattgctggacggacggcggcgcagCAATGGCGGTGATGGGCGGGAAGGAGTGGTTCTTCTACGTGCCGAGGGACCGTAAGTACCGGAACGGAGACCGCCCAAACCGGGTGACGGCGTCGGGGTA

upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G00650.1 (Glycine max), 3'ss of exon 1
gtacacttttctacatgaattccctcatccattttcatttcttaatttttgatgccctctctaccttcctttatttcctttttttttttttttctt-ttttatcatcaccatgcattcatctctcctgtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACCGCAAGTATCGAAACGGGGATCGCCCCAACCGGGTCACCACTTCTGGCTA
                                   |  ||    ||   |   |   | | ||  |   || |  |  || || |         || ||  ||  | | || | ||   | | |  |  ||||| |||| |||| || ||||| |||||||| |||| ||||||||||||||||||  | |||||||| ||||| ||||| ||||| || || || || ||||| ||
-----------------------------------ctcttacgcatacatatagatatttttatttcaattgagatgtttattgtgcacacggattgttgaattttaatcaagtatgtgtgtgtgtt--atgagcagCCTTGGCAGCTATTGGTGAGAAGGAGTGGTACTTCTATGTGCCCAGAGATAGGAAGTATCGCAACGGTGATCGTCCCAATCGTGTTACTACCTCTGGGTA

upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G40140.1 (Glycine max), 3'ss of exon 1
gtacacttttctacatgaattccctcatccattttcatttcttaatttttgatgccctctctaccttcctttatttcctttttttttttttttcttttttatcatcaccatgcattcatctctcctgtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACCGCAAGTATCGAAACGGGGATCGCCCCAACCGGGTCACCACTTCTGGCTA
                                    |  | | |  |  | |||  |  | ||  |   | ||| |   ||  | |||| ||||  ||     ||  | |||  || |  | |     ||||| |||| |||| || ||||| |||||||| |||| ||||||||||||||||||  | |||||||| ||||| ||||| ||||| || || || || ||||| ||
-------------------------------cgcatacatataaggtggtcatgtgcaatatatatatatatatatatattcatattttgtttcaattcacggatt-ctatgtcttgaattttg----atgagcagCCTTGGCAGCTATTGGTGAGAAGGAGTGGTACTTCTATGTGCCCAGAGATAGGAAGTATCGCAACGGTGATCGTCCCAATCGCGTTACTACCTCTGGGTA

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|71857846|gb|DT006901.1|DT006901
EST:     ACTCATTACCTCTCTAGATCTCTATCGCTATGACCCCTGGGAGCTGCCTG                         CCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACC
genomic: ACTCATTACCTCTCTAGATCTCTATCGCTATGACCCCTGGGAGCTGCCTGgtacactttt ... gtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACC
EST: gi|110386083|gb|EC950656.1|EC950656
EST:     ACTCATTACCTCTCTAGATCTCTATCGCTATGACCCCTGGGAGCTGCCTG                         CCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACC
genomic: ACTCATTACCTCTCTAGATCTCTATCGCTATGACCCCTGGGAGCTGCCTGgtacactttt ... gtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACC
EST: gi|71855590|gb|DT004645.1|DT004645
EST:     ACTCATTACCTCTCTAGATCTCTATCGCTATGACCCCTGGGAGCTGCCTG                         CCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACC
genomic: ACTCATTACCTCTCTAGATCTCTATCGCTATGACCCCTGGGAGCTGCCTGgtacactttt ... gtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACC
EST: gi|349823684|gb|FQ415094.1|FQ415094
EST:     ACTCATTACCTTTCTAGATCTCTATCGCTATGACCCCTGGGAGCTGCCTG                         CCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACC
genomic: ACTCATTACCTCTCTAGATCTCTATCGCTATGACCCCTGGGAGCTGCCTGgtacactttt ... gtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttttttcttttttatcatcaccatgcattcatctctcctgtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACCGCAAGTATCGAAACGGGGATCGCCCCAACCGGGTCACCACTTCTGGCTA
                                 ttcatctctcctgt  CT-rich tract
     tttttttcttttttat  TA-rich tract