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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagctactctcctaatgtttaaaaaagttagggttcatgcatctactcacccatgcatgagtgcacacacatgaatgctatccttttcccgacatgcaatctctttccaatctgttcattccaagtgagtggacggtgtatttgaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA

Basic information

species Vitis vinifera
transcript Vv04s0044g01290.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 4
gtatgagctactctcctaatgtttaaaaaagttagggttcatgcatctactcacccatgcatgagtgcacacacatgaatgctatccttttcccgacatgcaa-tctctttccaatctgttcattccaagtgagtggacggtgtatttgaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA
                                                                 ||   | |    ||  || |  | |       ||| || |||  ||  ||| || | |||  |             | |||||   ||||       |  || ||  ||| |    |   |||  |   || || || ||||| ||| | |||||||| ||||| ||||||||||| ||||| |||||||| |||||| | |||  |||  | ||| |||  |
-----------------------------------------------------------------tgttaagagggaaacactgtggtatatattgtatgaaaatctgattttaatttgct-atttta-------------tatatttttgcctg-------agtatgcttcattattcaata--cagTCTAGTGAGACGCTTTCAGTCTATCTCGAGTATGTTTCTGGGGGCTCTATCCATAAGTTGCTTCAAGAGTATGGTGCATTTGGGGAGGCAGTCCTTCGGA

upper sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g35700.1 (Oryza sativa), 3'ss of exon 4
gtatgagctactctcctaatgtttaaaaaagttagggttcatgcatctactcacccatgcatgagtgcacacacatgaatgctatccttttcccgacatgcaatctctttccaatctgttcattccaagtgagtggacggtgtatt-tgaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA
                                                                                       |||||  |    |   ||   ||    ||    || | ||    ||| ||  ||   || ||   ||  |  | |   |||||| ||  |  |     |||  ||| ||  |||| ||| ||||| |||||| ||| ||||| ||||| || || || ||||||  ||| |||||||| |||||||||||||| || |  |
---------------------------------------------------------------------------------------ttttcttgtttagttctcatcttttgttcgaagcacttcaga-aagtagaaagtactttgtgttgcttatactttctaattctgtatgtttttccatgcagACTGATGATGCACTTTCAATTTATCTGGAGTTTGTTTCTGGGGGCTCAATTCATAAATTACTTAGAGAGTATGGTCCTTTTAAGGAACCTGTGATCCGTA

upper sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G15870.1 (Glycine max), 3'ss of exon 5
gtatgagctactctcctaatgtttaaaaaagttagggttcatgcatctactcacccatgcatgagtgcacacacatgaatgctatccttttcccgacatgcaatctctttccaatctgttcattccaagtgagtggacggtgtatttgaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA
                                                          | |||  |  | | |    ||     | ||    ||   |||| || | | | |||       |    || |   || | |   |   | |     ||  |  || ||    |  || ||||||  ||||| ||||||||||| || ||||||||||| |||||||||||||| ||||| || || |||||||| ||||||||  |||| ||||| ||||| |||||||
----------------------------------------------------------gtatggctaaa-atattccaa----gttctgaatccattatgccatttatatacaaaaaaaaaaa---aaattgttgaatgagattcattatttcatttata-aatatatatg--tgccatgtttgcagGGAGAAGAAACACTTTCCGTTTATTTGGAATATGTCTCTGGTGGTTCTATTCATAAATTACTTCAGGAATATGGGGCCTTCAAGGAGCCTGTTATTCAAA

upper sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G16670.3 (Glycine max), 3'ss of exon 4
gtatgagctactctcctaatgtttaaaaaagttagggttcatgcatctactcacccatgcatgagtgcacacacatgaatgctatccttttcccgacatgca-atctctttccaatctgttcattc-caagtgagtggacggtgtattt--gaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA
                                                          | |||   | | |  ||    |   ||| ||||  | |  |  | | ||  |     | ||| ||  | |||  |||     |  | ||||         |   | |||| |  |  ||   |||||| |||||  |||||| |||| || || |||||||| |||||||||||||| |||||||| || |||||||| || |||||||| |||||||| ||||| |||||||
----------------------------------------------------------gtatgctagaatattcaaagtttaaatcgttttaaccatgtttatacctaatatagctgtgtgcacactcaaaagaggtattgaagaatttccattatcatgtatataac-taatatatatacatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTCCATTTAAGGAGCCTGTTATTCAAA

upper sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 4
gtatgagctactctcctaatgtttaaaaaagttagggttcatgcatctactcacccatgcatgagtgcacacacatgaatgctatccttttcccgacatgcaatctctttccaatctgttcattccaagtgagtggacggtgtatttgaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA
                                                                          |||  |   ||   || |  |   || |  || | | | || | |  |    || | | ||     || ||  ||  |  ||  || || ||    |  || ||||||  ||||| ||||||||||| || ||||||||||| |||||||||||||| ||||| || || |||||||| ||||||||  |||| ||||| ||||| |||||||
------------------------------------------------------------------------gtatggctaaaata--ttccatgttctgaatcctgtatgccatttatatacaaaaaataattgt----tgaatgagattc-atttatg-aatatatatg--tgccatgtttgcagGGGGAAGAAACACTTTCCGTTTATTTGGAATATGTCTCTGGTGGTTCTATTCATAAATTACTTCAGGAATATGGGGCCTTCAAGGAGCCTGTTATTCAAA

upper sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 4
gtatgagctactctcctaatgtttaaaaaagttagggttcatgcatctactcacccatgcatgagtgcacacacatgaatgctatccttttcccgacatgcaatctctttccaatctgttcattccaagtgagtggacggtgtatttgaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA
                                                                      |  |  ||||  || | ||||  | | ||   | || |   || ||           ||  | || |   | |   | | | |||   | |||| |  |  ||   |||||| |||||  |||||| |||| || || |||||||| |||||||||||||| |||||||| || |||||||| || |||||| | |||||||| ||||| |||||||
--------------------------------------------------------------------gtatgctagaataataccattttaaccatattttaactgtgcacactcaaaa------gagaaattgaagaatttccatcatcatgta--tataac-taatatatatccatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTTCATTTAAGGAGCCTGTTATTCAAA

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|110698751|gb|EE076609.1|EE076609
EST:     TCAGTCAACTTTCACATCCAAATATCGTTCGATACTATGGTAGTGAAATG                         GGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATC
genomic: TCAGTCAACTTTCACATCCAAATATCGTTCAATACTATGGTAGTGAAATGgtatgagcta ... atgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATC
EST: gi|161714297|gb|FC063543.1|FC063543
EST:     TCAGTCAACTTTCACATCCAA-TATCGTTCAATACTATGGTAGTGAAATG                         GGTGAAGAA-CACTATCAGTTTATT-GGAGTATGTCTCTGGTG-CTCTATC
genomic: TCAGTCAACTTTCACATCCAAATATCGTTCAATACTATGGTAGTGAAATGgtatgagcta ... atgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATC
EST: gi|71863025|gb|DT012080.1|DT012080
EST:     TCAGTCAACTTTCACATCCAAATATCGTTCAATACTATGGTAGTGAAATG                         GGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATC
genomic: TCAGTCAACTTTCACATCCAAATATCGTTCAATACTATGGTAGTGAAATGgtatgagcta ... atgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggacggtgtatttgaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA
                         ttgtaac  putative branch site (score: 2)
        tgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagctactctcctaatgtttaaaaaagttagggttcatgcatctactcacccatgcatgagtgcacacacatgaatgctatccttttcccgacatgcaatctctttccaatctgttcattccaagtgagtggacggtgtatttgaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA