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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgatgaacattagtgatgaaaaatcatatttttcaagttcttttttttttttaattatcaaatattccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG

Basic information

species Vitis vinifera
transcript Vv07s0005g05160.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------gtgagtcgatga-acattagtgatgaaaaatcatatttttcaagttcttt---tttttttttaattatcaaatattccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
                                                 ||  ||  ||   | |  | || || ||  ||  ||     |  || | |   | ||  |  | || |    |  |||||  |||||||||||||| || ||||| || |||||||| ||||| |||||||||||  |||| || ||| | || ||||||||||||||||||||||| ||||| 
gtagagtagtgcatacttcaaatgggaagtcttctatatgatgaatgttgtttgtgtatagtaaaagattggtggaacttcccatgaaatagtttatatgagtattgatgaacttttttttttctccttatagGTATGATGCTCATTCGGGTGGAGAGCGTGAAATTCAGAGAACCATGTTGGAGTTGCTTAATCAGCTGGATGGTTTTGATTCAAGGGGAGATGTTAAAGTT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 3
-------------------gtgagtcgatgaacattagtgatgaaaaatcatatttttcaagttcttttttttttttaattatcaaatattcc-ttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
                   | || |      | |  | || ||   || | | |  |  |||   |  | |   |||   | |        |  ||| |||||||||||||| || |||||||| ||||| || ||||| |||||||||||  || |||| ||| | || |||||||||||||| |||||||| ||||| 
ggtctttcccttcccggctgagatttttatgaaaaaaatgttgctgaagcttctagtgaaaggattaatatgagttttgctgtttctcgccctgttgtagGTATGATGCTCATTCTGGTGGTGAGCGTGAGATTCAGAGAACCATGTTGGAGTTGTTAAATCAGCTGGATGGTTTTGATTCAAGAGGAGATGTTAAAGTT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------gtgagtcgatgaacattagtgatgaaaaatcatatttttcaagttcttttttttttttaattatcaaatattccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
                                                                                       ||| |   |   |   |    | | ||   |  | |      ||  || || || ||  | ||  |||| | ||||||||||||||| ||||||||||| ||||||||||| |||||||| ||||||||  |||| ||||||||||| ||||| |||||||| || ||||| ||||||
gtaagttatcgagtatcagcttctggagtcactgttttaagacattttctatcctctttttccggatgtagttttttgttttgggaggaggcagggggtacaggactggtagaagagtgatatcatgagtcaattcttattatatgtctcttatatgctttgcagGTATGATGCCCACTCAGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTCGATTCAAGAGGTGATGTTAAAGTG

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------------gtgagtcgatga-acattagtgatga-aaaatcatatttttcaagttcttttttttttttaattatcaaatattccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
                                                                                 | | |  |  ||  |   | || | | | | | ||||  |    | ||  || ||  | ||  | ||   ||| | ||||||||||||||| ||||| ||||| ||||||||||| |||||||| ||||||||  |||| ||||||||||| |||||||||||||| ||||| || ||||| 
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcat---ggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 3
-----------------------------------------gtgagtcgatgaacattagtgatgaaaaatcatat----ttttcaagttcttttttttttttaat--------tatcaaatat-tccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
                                         | |  | || ||    | ||  || |  |   |||    | ||    |||||||  |   || ||        ||  |||||| |  || ||||||||||||||||||||| || ||||||||||| || ||||||||| | ||  |||| ||||||||||| |||||||||||||| |||||||| ||||||
gtaattttaacctccaactttagtattcatgaaggtagggtggggttggaagagtgat-gtcttgtatcactctatgagctcttaggattcttttcctacattcatgagcttactaataaatatgtatttacagGTATGATGCTCACTCAGGAGGAGAACGTGAAATTCAAAGGACCATGCTAGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGATGTGAAAGTG

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 3
---------------------------------------gtgagtcgatgaacattagtgatgaaaaatcatat----ttttcaagttcttttttttttttaattatc--------aaatat-tccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
                                       | |  | || ||    | |   || |  |   |||    | ||    |||||||  |   || || | |        |||||| |  || |||||||||||||||||||||||| |||||||| || || ||||||||||| ||  |||| ||||||||||| ||||||||||| || |||||||| ||||||
gtaattttaacccccaactttagctgtcatgaaggtaccggggatggaagagtgat-gccttgtatcactctatgagctcttgggattcttttcctacattcatgagcttaccagtaaatatgtatttacagGTATGATGCTCACTCAGGTGGAGAACGTGAGATTCAAAGGACCATGTTAGAGTTGCTGAACCAGTTAGATGGTTTTGATTCTAGAGGAGATGTAAAAGTG

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------------gtgagtcgatgaacattagtgatgaaaaatcatatttttcaagttcttttttttttttaattatcaaatattccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
                                                                                        |||| |  | |||  | |  |  || |    || |    ||| |  || || || ||  | ||  |||| | ||||||||||||||| |||||| |||| ||||||||||| |||||||| ||| ||||  |||| ||||||||||| ||||| |||||||| || ||||| ||||||
gtaagttatcaagtatcagcttctagagtcactgttttaagacattttctatcctctttttccggatgtagtttttttgttttgggaggagtaggggtacaagactagtagaagagtg-atatcatgagt-caattcttattatatgtctcttatatgctttgcagGTATGATGCCCACTCAAGTGGAGAACGTGAAATTCAGAGGACTATGATGGAGTTGCTGAACCAGTTAGATGGTTTCGATTCAAGAGGTGATGTTAAAGTG

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtcgatgaacattagtgatgaaaaatcatatttttcaagttcttttttttttttaattatcaaatattccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
|| |||  |   |  ||  | |     |   |||         |  |  || | |  | | |      |        ||||||||| ||||||||||| ||||||||||| ||||| || || ||||||||||| || |||||| | || || ||||||||||| |||||||| || || 
gtaagttaaactattttcataaacctgatctataacccattgataatggttatctgattacttgttgtttgaaagaacagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 3
----------gtgagtcgatgaacattagtgat-gaaaaatcatatttttcaagttctttt-----ttttttttaat------tatcaaatattccttg---cagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
           |    | || ||||| |   || || |||  || || || |  ||  |       |  | | ||||      ||| ||||  |  |||   ||||||||| ||  |||||||||| |||||||||||||| || |||||||||||||| || |||||| | || || ||||||||||| |||||||| || || 
gtatgcctaaatacaac-ataaacatgatccattgataaacaatgttcttgattttgctcaagagatggtatctaatatgtgatataaaatggtggttgaaacagGTATGACGCAAACTCAGGTGGGGAACGTGAAATCCAAAGAACCATGTTGGAACTACTGAACCAGCTTGATGGGTTTGATTCAAGAGGAGATGTTAAGGTT

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------gtgagtcgatgaacattagtgatgaaa------aatcatatttttcaagttcttttttttttttaattatca--aatattcc-ttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
           |||  | | |  | | |  |||| | |      |||  | | |   ||  |  | | || |   ||||| ||    || | | |||||| ||||||||||| |||||||| ||| | || || |||||||| ||||||||  |||| || ||||| || || ||||||||  | |||||||| || || 
agcggcgtgtcgtggtttggtttatagttctgattacagtcataaattctgtctagtaatcttgtctattctgaaaattaacattggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT

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|27580875|gb|CB003570.1|CB003570
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|110703456|gb|EE080320.1|EE080320
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|30321368|gb|CD004630.1|CD004630
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|110713467|gb|EE089413.1|EE089413
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACCAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGGAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|71880466|gb|DT029521.1|DT029521
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACT
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACT
EST: gi|110356778|gb|EC919853.1|EC919853
EST:     CACCTTTCA-TTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAG
genomic: CACCTT-CAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAG
EST: gi|26264508|gb|CA815571.1|CA815571
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|27580357|gb|CB003052.1|CB003052
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|71880867|gb|DT029922.1|DT029922
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCA
EST: gi|161714191|gb|FC062936.1|FC062936
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAA-GAG                         GTATGATGCTCA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCA
EST: gi|30297307|gb|CB974101.1|CB974101
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|27580606|gb|CB003301.1|CB003301
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|30131170|gb|CB916509.1|CB916509
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|71864574|gb|DT013629.1|DT013629
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|110392599|gb|EC958132.1|EC958132
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
EST: gi|71881961|gb|DT031016.1|DT031016
EST:     TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAG                         GTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA
genomic: TCACCTTCAATTGTCTTCATTGATGAAATTGATGCAGTTGGTACAAAGAGgtgagtcgat ... ttccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatcatatttttcaagttcttttttttttttaattatcaaatattccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG
                             ttttaat  putative branch site (score: 3)
                                           tattcctt  putative PPT
      atatttttcaagttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgatgaacattagtgatgaaaaatcatatttttcaagttcttttttttttttaattatcaaatattccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG