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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG

Basic information

species Vitis vinifera
transcript Vv06s0009g03520.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os05g36070.2 (Oryza sativa), 3'ss of exon 7
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagt----ttgtttgtacttctaagtgatttttgacatgg-gtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
     ||  |     ||      ||||| | |        | | |||  ||       |||  | || ||| |  | | |  | |||  | |      | | |||   ||||| ||| | |||||||||||||||||||||||||||||||| |||||||||||||| ||||| || |||||||| || |||
-----gcttgcgaaattaaagtccatatttgtatacaccaccgtattgtgtaaagcatttttaatttgtaacttttgtgtatcgtggtattcccttttaattcagAGCGGACTCTTTTTCTATGATATTTTCTGGGTCTTCTTCACTCCAGTTATGGTCAGTGTTGCCAAGTCATTTGATGCTCCAATAAAG

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttt-tgacatggg---tacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
    ||  | ||||| |       ||  |  ||| || |      |  |  |   |  ||  |   |  | || | |  || |||   | |||    ||| ||||| || || ||| | ||||||||||||||||| ||||||||||| || ||||||||||||||||| || || ||||| || || |||
--cctgtta-tatttgtagaaactattgcactgcttgctgtactttgtaaatcactattaagttgtaacgcttatgtatcacgggatttcctttttgatt-cagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
----ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
    |||  || ||   ||   |          | ||  |  |  |   ||||  ||  ||  | |  || || | |    |  |      || |   || ||||  ||||||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| || || || ||||||||||| || |||
gtaattggggctagcccttgcattttgagagcatctgaattattttatgttca--ttaattacattcatatgtaaatgc--atttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G150251_T01 (Zea mays), 3'ss of exon 7
---ttgatgccagtatttttgtccctcatatctatgcctgttc-ctgcattcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
   |||||  |  | |  ||||   |||    | |||| ||         || |||  ||  ||| |  |  || |   ||  || |    || | | || ||||  ||||||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| || || || || ||||||||||| |||
gagttgatttct-tctacttgtt--tcaacattgtgccagtgaatcattctctgttcattattacatgcatatg-tgaatgcaattgtccttttccatttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAG

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaat---------tgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
         |      |     |||||| | |         ||  ||   ||  ||| | | |||   || | ||||   ||  |  || | |||         ||||||| ||||| ||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||| || || |||||||| || |||
---------gctacaataagattcatatttgttttgtaatttgtttttcattcattttttcatcttcatggtctttgctttgaatcttttccaatctcatgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G08620.2 (Glycine max), 3'ss of exon 7
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcatt-cagtttgtttgtacttctaagtgatttttgaca----tgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
     | |||| | ||      ||| |  ||||| | |   || ||     | | ||| |  ||| |  || | ||||||     |   | | ||    || ||||| || || ||||| ||||| ||||||||||| |||||||||||||||||||| || |||||||| || || |||||||| || |||
----agtcagt-tattaaaagatcaaacatatgcttttcattgtataattctctctttttgtttcaatatggtctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTTAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgaca----tgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
||  |  |||| | ||      | |    ||||| | |   || ||  | |   ||| |  ||| |  |||| ||||||     |   | | ||    || ||||| || || ||||| ||||| ||||||||||| |||||||| |||||||||||||| |||||||| || || |||||||| || |||
ttagt--cagt-tattaaaagattaagcatatgcttttcattgtata-actccttttttttttcaatatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------ttgatgccagtatttttgtcc-ctcatatctatgcctgttcctgcattcagtttgtttgtactt--ctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
              ||        |||| |||    ||  | |  |   ||        |   | || ||||| |  |  || | | |||       ||  ||     || |||||||||||||| ||| | |||||||| |||||||| ||||| |||||||| ||||| |||||||| || |||||||||||||| ||||||
gtaagaactgcatcttttgaatgctattcttgaaaacttgtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgt-tatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S47_5V6.2 (Physcomitrella patens), 3'ss of exon 7
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgattttt-gacatgggtacttgcga---attgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
     |   || |           | |    ||  | ||       | | || |    || ||      || |||  ||  | |||  |  |||   | ||||||||||||| ||  | || || || |||||||| |||||||| || || ||||| || || |||||||| ||||||||||| || |||
----ggtttgtgtgaaaaggtgcaagagtgttgagttttgggattgtaaattggcaattaattggggaggagtttgagatgttggtggtcacgatggagtgcagGCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ18240 (Selaginella moellendorffii), 3'ss of exon 6
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgta-cttctaagtgatttttgacatgggtacttgcgaattgc-agGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
                                      | | |  |||| ||       | |   |   |||||| |    |   |   |  |  | || |||| || || || || ||||| || |||||||| ||||||||||| ||||||||||  ||||| |||||||| |||||||| || |||
-------------------------------------gtaccgtgttcacttacaaaacaacactttgatgatttgt----tttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
                                      | | |  |||| ||       |   ||   ||||  ||    |     ||         ||||| || || || || ||||| || |||||||| ||||||||||| ||||||||||  ||||| |||||||| |||||||| || |||
-------------------------------------gtaccgtgttcacttacaaaacaacactt--tgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG

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|71877015|gb|DT026070.1|DT026070
EST:     GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG                         GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
genomic: GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTGgtaagaacct ... cgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
EST: gi|27579299|gb|CB001994.1|CB001994
EST:     GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG                         GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
genomic: GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTGgtaagaacct ... cgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
EST: gi|110391760|gb|EC956760.1|EC956760
EST:     GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG                         GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
genomic: GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTGgtaagaacct ... cgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
EST: gi|110361505|gb|EC924984.1|EC924984
EST:     GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG                         GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
genomic: GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTGgtaagaacct ... cgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
EST: gi|77579348|gb|DV218502.1|DV218502
EST:     GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG                         GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
genomic: GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTGgtaagaacct ... cgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
EST: gi|161717568|gb|FC066896.1|FC066896
EST:     GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG                         GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
genomic: GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTGgtaagaacct ... cgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
EST: gi|349812621|gb|FQ409780.1|FQ409780
EST:     GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG                         GCAGGACTTTTTGTTTATGATATTT
genomic: GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTGgtaagaacct ... cgaattgcagGCAGGACTTTTTGTTTATGATATTT
EST: gi|110730433|gb|EE107509.1|EE107509
EST:     GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG                         GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
genomic: GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTGgtaagaacct ... cgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
EST: gi|110708740|gb|EE086629.1|EE086629
EST:     GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG                         GCAGGACTTTTTGTTTATG
genomic: GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTGgtaagaacct ... cgaattgcagGCAGGACTTTTTGTTTATG
EST: gi|71874644|gb|DT023699.1|DT023699
EST:     GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG                         GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG
genomic: GTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTGgtaagaacct ... cgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
                           ttttgac  putative branch site (score: 3)
                       tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- gatgcca
- - - - - - - - - tccctca
- - - - - - - - - - - - - - ctatgcc
- - - - - - - - - - - - - - - - - - - tcctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatggg