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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA

Basic information

species Vitis vinifera
transcript Vv06s0004g00240.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 2
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA
                        |||    ||  |||| |  ||||     |     |||   |   || |   | ||| | ||  | |||  | || |||    |||| || |  |||| |||||| ||||| ||||||||||| || ||||| || ||||||||||||||  ||||||||||||| |||||||||||||| || || |||||||| |
-----------------------gtgagttgtacattctaataatttctactagcatgatgctatcatctat---aacatcaacttctgagttgtgacttct----attttctatgacagAATGGAGTCAATAAGCTTGCTGATCTCGTTGGAGTCACCCTTGGTCCAAAAGGACGGAATGTTGTCCTTGAGAGCAAGTATGGATCACCTAAAATTGTCA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaac--attttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA
                      |  | || | |  |  || ||  || || |  | |  |    | ||   ||  |   | | | |    | |  ||  |||   | | ||     | ||||||||||||||| || |||||||| || || |||||||| || || ||||| || |||||||||||  | |||||||||||||| ||||| |  ||||| |
---------------------gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgacc----aggcact--cattagttatttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G133698_T02 (Zea mays), 3'ss of exon 2
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctt--tttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA
                               |  | ||   |  |||| || |||   || ||   || || ||| | |   |     | |  ||||    |||   |  |||   |||||||||||||| ||||| ||||| || ||||| |||||||| || || ||||| || |||||||||||  | |||||||||||||| || || ||||||||||
------------------------------gtgagctccacagtttttatttattatgatatacc-gatttgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 2
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattc----ctatgtatta-gactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA
                         |   |    | |  |  || | | ||  ||     | ||||| |  | | | ||  |||  |     ||| |  |    || |    ||   | | |||||||||||| ||||| ||||| || ||||| |||||||| || || || || || |||||||| ||  | ||||||||||| ||||| || || |||||||
-------------------------gtgaagcgagcttcgggcactcttttatttgaagacgatgtactgtggcctcct--tcaccaggcactaa-ttgtgttttcgtcttcttctgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G015989_T02 (Zea mays), 3'ss of exon 2
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA
||||||||   | | | | || | | || |   |   || |       | || | |  | ||   ||  |   |     |||  | |||             || | |||||| | ||||| ||| || || || ||||| ||||| || || ||||||||||| ||||| ||  | ||||| ||||| || |||||||||||||| || |||||||| |
gtgagttt---tctgacaaacatataataacgcttgactaaggccgccgctgctcctcacgttcaagtgtgcgttgcacttacttatta------------cttgattttcctatgtcagAATGGGGTCAACAAGCTTGCAGATCTCGTCGGGGTTACTCTTGGACCAAAGGGGCGAAATGTAGTCCTCGAAAGCAAGTATGGCTCACCTAAAATTGTCA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctatgtattagactttctgatcattatctcttaagtcc-taacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA
                                             |  ||  |||| ||| |    || ||| |||    ||  |||| | |   |||| | | ||| |||| || |  || |||| || ||||||||||| ||| |||| || |||||| | ||||| ||||||||||||||||| ||||||||||| || || ||||| | ||| ||||
--------------------------------------------gtgagtctattc-tatttcggtgattttgtgacttctagttctttattgaataacttatatca-tttcattatgtagGCTGGTGTGAATAAACTTGCGGATTTAGTTGGGGTTACTTTAGGTCCTAAAGGCAGGAATGTTGTTCTAGAGAGCAAATACGGTTCCCCTAGAATCGTTA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA
                                  ||    |  | |   ||||||     |  | |   ||     || || | | ||  ||      ||   ||  ||    || | ||||||| || || || || || || || || || || || ||||| |||||||| || |||||||| || |||||||||||||| ||||||| ||||||||
----------------------------------gtgagaattaatgaattgattttctggagtaatgattaggattcgttttatttttggtttctg-attactcgtttg---ttattagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctat--gtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA
                                 | | | ||| |  ||  |   ||  ||  | ||| | |  | ||   | | | |||||       || | || | |          ||| ||||||| || || || || ||||| || ||||| ||| | ||||| ||||| |||||||| ||||| |||||||||||||| || ||||| ||| | |
--------------------------------gtttgcagaaaagcttcctctctcggattggcattgggccat-tggcgagtttttctta----tcgactttttgcgaaa--------cagGCTGGAGTGAACAAGCTCGCGGATCTTGTTGGAGTGACTTTGGGTCCCAAAGGAAGGAATGTCGTCCTCGAGAGCAAGTATGGTTCTCCAAAGATTATCA

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|110685246|gb|EE063449.1|EE063449
EST:     CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
EST: gi|110725842|gb|EE102769.1|EE102769
EST:     CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACACTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
EST: gi|351022807|gb|FQ428716.1|FQ428716
EST:     CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACACTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
EST: gi|110699104|gb|EE077129.1|EE077129
EST:     CTAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
EST: gi|351024818|gb|FQ430643.1|FQ430643
EST:     CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACACTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
EST: gi|349833403|gb|FQ420149.1|FQ420149
EST:     CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACACTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
EST: gi|29782617|gb|CB348122.2|CB348122
EST:     CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
EST: gi|30256253|gb|CB972096.1|CB972096
EST:     CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
EST: gi|110689447|gb|EE065678.1|EE065678
EST:     CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
EST: gi|351040630|gb|FQ438174.1|FQ438174
EST:     CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACACTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA
EST: gi|351025708|gb|FQ426722.1|FQ426722
EST:     CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAG                         ACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACACTTGGTCCAAAA
genomic: CAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgt ... cctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA
                          tcctaac  putative branch site (score: 1)
                                catctttcaatttcct  CT-rich tract
                                    tttcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG