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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT

Basic information

species Vitis vinifera
transcript Vv04s0008g03720.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 3
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattct-gcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
        ||     | |  ||||  ||||| || | || |   ||  |||| |   | ||  |      | || | || | |||| |    ||| ||| |||||  | |||||| ||||||| |||| | | |||||||||| ||||||||||| || || |||||| | |||||||||||||| |||||||| || |
--------gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaata------tgatggcatatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
                          | |  |  |   |||| || |  || | |  | || | |       || | ||||||| |      ||  |||||||||  ||||| | |||||||||| | ||||||||||| |||||||||||||||||||| ||  |  | ||||||||||| ||||| ||||  ||||
-------------------------gtctgctaacactgtttgatgtccttccatg-ctgaaagattaagatattg-atttattgttttgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g17350.2 (Oryza sativa), 3'ss of exon 3
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagta----tttattctgc-aaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
            |     ||  | |||     |    ||||  | || | |  |||   |  ||  || |  ||  ||     |||||||    |  ||  |||||||||| ||||| | |||||||||  | | ||||||||| ||||||||||||| |||||| ||   | | |||||||||||||||||||| || ||||
-----------gtatgtatataagtttaaaccttaaaagttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttgagcttttagCCTGATTTTCATGTGAAAGAGAAGATCCTCACTCTGATAGACACTTGGCAAGAAGTTTTTGGCGGGGTACGTGCAAGATATCCACAATACTACGCAGCAT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatt--tattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
            ||||| ||    |||  || |  | |   ||   |  ||| |     ||    |  | | ||  |  |  | |  |   |  || ||| |||||   | ||| | ||||||  ||||| | ||||||||||| ||||||||||| ||||| |||||| | ||||||||||||||||||||||| ||||
-----------gttcaa-tatg--tttcatgcttgcaaaactctacttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------gtcagact---gtcattcaagtaccatttttttgttccctagtttcatttattta--cttatccg------agaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
                                                             || | |    ||||      || | ||| |||     |  ||     ||  ||  | ||| |       | ||   |||  |   || |  |||     |  || ||||||| |  || |||| |||||||||||| ||||||||||| |||||||||||||||||||| ||  |  | ||||||||||| || || || || ||||
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
                 |||   |   |   ||    |  || ||||| | | |      || ||    || ||  | | | || || ||||||  ||| |||||  ||||| | |||||||||  | |  |||||||||||||||||||||| |||||| ||  || | ||||||||||||||||| ||||| ||||
-----------------gtat-gtgcatacattttaaaccttaatttactgattgtcaatagcaaatccttaatgct-tctcttttg-aaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G062953_T02 (Zea mays), 3'ss of exon 3
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttc---atagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
            ||||| ||    ||  |  || |  |  |  | ||  ||| |     ||    |  |||    || | ||||  | | ||   || ||| |||||   | ||| | ||||||| ||||| | ||||||||||| |||||||| |  ||||| ||| ||   ||||||||||||||||||||||| ||||
-----------gttcaa-tat-gcttcatgcttgcaaaactgtagtt-cttattctaatgaactgctggtttctgatggcattttgttttcatg-ttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAAGACGTGTTTGGGGGATCACATGCAAGATATCCACAATACTATGCAGCAT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
gt-cagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
||  | |  ||   |  | ||   |||||  |||  ||| | ||  |  |||  | ||   | | |  |||| ||   |||| |  | | || ||| |||||||||| ||||||| |||||||||| ||||||| ||||||||||||||||||||||||||||| || |||||||||||||||||||| |||||||| |
gtatacatagtttcttgaatat--tttttcagttttctaatgtctctgttttcttcat---atatatatgttgatgtcatttgtcataccaa-ttgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
gt-cagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
||  | |   |   |  | ||   ||||   | |  ||  | |   |  |||  | ||  |  |||  |||| ||   |||| |  ||| || ||| |||||||||| ||||||| ||| |||||| || ||||  |||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||
gtatacataatttcttgaatat--ttttgcagctttctgatgtttctgttttcttcat--gtaaaatatgttgatgtgatttgtcatgccaa-ttgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 3
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgt-tcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
                 |||    || ||       | || ||  ||  |  ||     |     ||| | | ||  || ||  ||||    ||   |||| || || ||||||| |||||||||  || | || || ||||| |||||||| || ||||| || || |||||||||||||||||||||||||| | ||
-----------------gtaatggttcttc-caaattggtctctctttctctctcccttgctctgcctctctaatcctaattggtctgatgcat-atagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT

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|352764099|gb|FQ467669.1|FQ467669
EST:     TAGCAGAGAGAGATATTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG                         CCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAA
genomic: TAGCAGAGAGAGATATTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtcagactgt ... aaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAA
EST: gi|33406474|gb|CF212101.1|CF212101
EST:     TAGCAGAGAGAGAT-TTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG                         CCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAA
genomic: TAGCAGAGAGAGATATTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtcagactgt ... aaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAA
EST: gi|18459792|gb|BM438070.1|BM438070
EST:     TAGCAGAGAGAGATATTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG                         CCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAA
genomic: TAGCAGAGAGAGATATTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtcagactgt ... aaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT
                          ttcatagtatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC