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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctgaatgaaatttcaagaacctagaattcttcaggcctgtcatatctataattatttttaagattcaccctaaatttaatttttcacatttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGGATGTCTGCCATGGATAGCTCCAGCAGAAATGCTGGCGATATGCTTGATC

Basic information

species Vitis vinifera
transcript Vv17s0000g07300.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g07300.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os10g17280.1 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------------------atctgaatgaaat----ttcaagaacctagaattcttcaggcctgtcatatctataattatttttaagattcaccctaa----atttaatttttcacatttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGGATGTCTGCCATGGATAGCTCCAGCAGAAATGCTGGCGATATGCTTGATC
                                                                  |  ||| || |    | ||  |   || |  |   |      |  |   | || ||| |||||   |   | ||||     || | || |||    |||    |||||| |||  |||||||   |||||||||| ||||||||||  || ||  | |||||||||||||| |||||||||||||| ||||| || ||||||||||
gtaagtttgtcttcattaatcatatatacctctcaatagatgaattagctacaactattacagccacaaaatcaagtcgcatccataagggtaaacgttccctttgtagagagcgcaatcattcttttttcaaggtatcctagtggtatcttatgtttttgctttgtggcagGTTATGTATAATGCTGCTCTAGAGAATGCATGCAGTGAGCTTGGAGCACGTATGTCTGCCATGGACAGCTCCAGCAGAAACGCTGGTGAAATGCTTGATC

upper sequence: Vv17s0000g07300.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G321725_T03 (Zea mays), 3'ss of exon 3
-----atctgaatgaaatttcaagaacctagaattcttcaggcctgtcatatctataattatttttaagattcaccctaaatttaatttttcacatttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGGATGTCTGCCATGGATAGCTCCAGCAGAAATGCTGGCGATATGCTTGATC
     |  ||  | | ||| || |||  | |     ||  ||  |   |  |  |||||| | | |    |        |  ||    | ||     | |  |||||  ||| ||||| ||   |||||||||| ||||||||||  || ||  | |||||||||||||| ||||| ||||||||||||||||||||||||||||
caggaaaatgtgtaacattccatgaatttgg----ttttgggtttaagac-tagataattttgtctcccttattgtaatatattgccatgtctggcgtactgcagGTCCTGTACAATGGTGCCCTAGAGAATGCATGCAGTGAGCTTGGAGCCCGTATGTCTGCCATGGACAGCTCTAGCAGAAATGCTGGCGATATGCTTGATC

upper sequence: Vv17s0000g07300.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G009638_T01 (Zea mays), 3'ss of exon 2
atctgaatgaaatttcaagaacctagaattcttcaggcctgtcatatctataattatttttaagattcaccctaaatttaatttttcacatttccc----tcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGGATGTCTGCCATGGATAGCTCCAGCAGAAATGCTGGCGATATGCTTGATC
   |  | |||| ||  |  |  |  |    || |    ||     | ||  | ||  |       || |||| | | |||| | |  || |  |     ||||||  ||| ||||| ||   |||||||||| ||||||||||  || ||  | |||||||||||||| ||||| ||||||||||||||||||||||||||||
--atacaggaaaattgtaccatttccatgaatttatttttg--gggtttaagactagataattttgtctcccttattgtaatatattgcaatgtctgacttcagGTCATGTACAATGGTGCCCTAGAGAATGCATGCAGTGAGCTTGGAGCCCGTATGTCTGCCATGGACAGCTCTAGCAGAAATGCTGGCGATATGCTTGATC

upper sequence: Vv17s0000g07300.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G22050.4 (Glycine max), 3'ss of exon 7
----atctgaatga-aatttcaagaacctagaattcttcaggcctgtcatatctataattatttttaagattcaccctaaatttaatttttcacatttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGGATGTCTGCCATGGATAGCTCCAGCAGAAATGCTGGCGATATGCTTGATC
    || |   |    ||||  | |   ||   |  ||      | |    | |   || ||  |  |  || |   | |   || |||   | || |     ||||  ||| ||||||||| || ||||||||||| ||||||||||| || || |||||||| ||||| ||||| ||||| |||||||| |||||||||||||
ttttatatacctattgatttagaaatgttatcttgatttgaaagtctttcttttgacatcatggtctacttttatttttacactactttgctatatat-----agGTCATGTACAATGCTGTGTTGGAGAATGCTTGTAGTGAGCAAGGAGCAAGAATGTCTGCAATGGACAGCTCTAGCAGGAATGCTGGGGATATGCTTGATC

upper sequence: Vv17s0000g07300.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G32460.1 (Glycine max), 3'ss of exon 7
----atctgaatgaaatttcaagaacctagaattcttcaggcctgtcatatctataattatttttaagattcaccctaaatttaatttttcacatttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGGATGTCTGCCATGGATAGCTCCAGCAGAAATGCTGGCGATATGCTTGATC
     | ||  |    |||     ||||||  |    |  |  |||| | |||  |  |  |  |    |||    ||  ||||   |       |     |||||  ||| |||||| || || |||||||| || ||||||||||| || || |||||||| ||||| ||||| ||||| |||||||| |||||||||||||
ctagctttgtgttttcttttttatacctagtttgaaactag--tgtcctttcttcagatcatgctctacttc--tttatttttacactactttgctatgtgcagGTGATGTACAATGCCGTGTTGGAGAATGCCTGTAGTGAGCAAGGAGCAAGAATGTCTGCAATGGACAGCTCTAGCAGGAATGCTGGGGATATGCTTGATC

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|110378840|gb|EC943994.1|EC943994
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
EST: gi|34320546|gb|CF373300.1|CF373300
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
EST: gi|110393077|gb|EC957966.1|EC957966
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
EST: gi|33402169|gb|CF207796.1|CF207796
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
EST: gi|71868993|gb|DT018048.1|DT018048
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
EST: gi|110407251|gb|EC972848.1|EC972848
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
EST: gi|110425845|gb|EC992238.1|EC992238
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
EST: gi|26264079|gb|CA815142.1|CA815142
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
EST: gi|37189009|gb|CF608358.1|CF608358
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCAAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
EST: gi|110701285|gb|EE078691.1|EE078691
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
EST: gi|110366906|gb|EC930825.1|EC930825
EST:     AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGT                         GTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG
genomic: AGACGAAGGGAGAAATACTTCAGAACCTAGCGGAGTTCCAGTTTTCTTGTgtaagtccta ... tttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctataattatttttaagattcaccctaaatttaatttttcacatttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGGATGTCTGCCATGGATAGCTCCAGCAGAAATGCTGGCGATATGCTTGATC
                                    tttttcacatttccct  CT-rich tract
     taattatttttaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctgaatgaaatttcaagaacctagaattcttcaggcctgtcatatctataattatttttaagattcaccctaaatttaatttttcacatttccctcagGTTTTGTTCAATGCTGTATTAGAGAATGCTTGCAGTGAGCAAGGTGCGAGGATGTCTGCCATGGATAGCTCCAGCAGAAATGCTGGCGATATGCTTGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - -aatgaaa
- - - - - - - - aagaacc
- - - - - - - - - - - - - - - cttcagg
- - - - - - - - - - - - - - - - - - -cctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcaccc