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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgtcagatatttttttaaagtttttaatttataatggtggttaaatctacggaaaaaaaatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATATTTTCTGGAGCTGGGGGTCATCGCAATGAAGTCTTGAGTGTG

Basic information

species Vitis vinifera
transcript Vv19s0014g05210.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g04270.1 (Oryza sativa), 3'ss of exon 5
-gtaggtgtcagatattttt----ttaaagtttttaatttataatggtggttaaatctacggaaaaaaa-atcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATATTTTCTGGAGCTGGGGGTCATCGCAATGAAGTCTTGAGTGTG
  | |  |  ||   ||| |     |  |  |||  || | ||||  |   | | |||     | |    ||     ||||||| || ||  || | |||||||||||||| || || ||||||||||| ||| ||||||| || ||||| || |||||||| |||||||| 
gtttgaagatagccttttctggagctggatctttctatgtttaattatttctgattctgtttcacatggcattgcatagGATGAATCTGTTAGGCTGTGGAATGTTCACACAGGGATCTGCATTTTGATTTTTGCTGGAGCAGGAGGTCACCGGAATGAAGTATTGAGTGTT

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G148924_T03 (Zea mays), 3'ss of exon 4
-------------------gtaggtgtcagatatttttttaaagtttttaatttat---aatggtggttaaatctacggaaaaaaaatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATATTTTCTGGAGCTGGGGGTCATCGCAATGAAGTCTTGAGTGTG
                    ||||| |||  ||  ||||||   ||| |||| | |   |||  ||     || |        |  ||| |  ||||||| || ||  || |||||||||| || || || || || || ||||||||| |||||||||| ||||||||||||||||| |||||||| 
gttatgcgatagtctgttcttaggt-tcatgtacctttttatt-tttataatctttctgaattttgacaccatttcatatggcattatctaataggatgaatctgttagGCTATGGAATGTCCATACAGGGATCTGTATCTTGATATTTGCTGGAGCTGGAGGTCATCGCAATGAAGTATTGAGTGTT

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G36310.1 (Glycine max), 3'ss of exon 4
gtaggtgtcagatatttttttaaagtttttaatttataa-tggtggttaaatctacggaaaa-aaaatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATATTTTCTGGAGCTGGGGGTCATCGCAATGAAGTCTTGAGTGTG
|||  |      |   | |||  | | | ||| | ||   | ||  || | || | |      ||  |  | |||||||| ||  | ||||||||||||| ||| || ||||||||||||||||||||| ||||||  ||||| ||||| ||||||||||| ||||| 
gtaaatagtttctccatattttcactatctaaataatcccttgtttttcattcgatgacttctaaggtttatcagGATGAATCTATTCGGTTATGGAATGCTCATACTGGAATATGCATTTTGATATTTGCTGGAGGCGGGGGACATCGTAATGAAGTCTTAAGTGTT

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G17110.1 (Glycine max), 3'ss of exon 4
gtaggtgtcagatatttttttaaagtttttaatttataa-tggtggttaaatctacggaaaa-aaaatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATATTTTCTGGAGCTGGGGGTCATCGCAATGAAGTCTTGAGTGTG
|||  || |   |   | |||  | | |||||   ||   | ||  || | || | |  |   ||  |  | |||||||| || || ||||||||||||||||| || |||||||||||||| |||||| | |||||||| || ||||| ||||||||| | ||||| 
gtaaatggcttctccatattttcactatttaaaaaatcccttgtttttcattcaatgacatctaatgttgatcagGATGAATCTGTCCGGTTATGGAATGTTCATACTGGAATATGCATTTTAATATTTGCGGGAGCTGGAGGACATCGTAATGAAGTCCTAAGTGTT

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G02690.1 (Glycine max), 3'ss of exon 4
gtaggtg--tcagatatttttttaaagtttttaatttataatggtggttaaatctacggaaaa-aaaatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATATTTTCTGGAGCTGGGGGTCATCGCAATGAAGTCTTGAGTGTG
|||  ||  |     || |||| | | |||  |   |  | || |  || | || | |  |   ||  |  | |||||||| || || ||||||||||||||||| || |||||||||||||| |||||| | |||||||| || ||||| |||||||| || ||||| 
gtaaatggcttctccatattttcataatttaaagaatccattgttt-ttcattcaatgacatctaaggttgatcagGATGAATCTGTCCGGTTATGGAATGTTCATACTGGAATATGCATTTTAATATTTGCCGGAGCTGGAGGACATCGTAATGAAGTTTTAAGTGTT

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G34240.1 (Glycine max), 3'ss of exon 4
gtaggt-gtcagatatttttttaaagtttttaatttataatggtggttaaatctacggaaaaaaaatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATATTTTCTGGAGCTGGGGGTCATCGCAATGAAGTCTTGAGTGTG
|||  | |    |||||||    |  |    |||   | ||  |  || |||       ||     |  | |||||||| ||  | ||||||||||||| ||| || ||||||| ||||||||||||| |||||||  |||| ||||| ||||||||||| ||||| 
gtaaatagcttcatattttcactatttaaagaatccctcattttcattcaatgacttctaagg---tttatcagGATGAATCTATCCGGTTATGGAATGCTCATACTGGAATATACATTTTGATATTTGCTGGAGCCAGGGGACATCGAAATGAAGTCTTAAGTGTT

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G20740.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------gtaggtgtcagatatttttttaaagtttttaatttataatggtggttaa-atctacggaaaaaaaatc-aaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATATTTTCTGGAGCTGGGGGTCATCGCAATGAAGTCTTGAGTGTG
                  |     ||  | | | |  | |  | |||  | | |  ||||| |||| | ||          |||  ||  ||||||| || || || || ||||||||| | || || ||||| |||||||||||| |||||||||| ||||||||| |||||||  | ||||||
gtatatctcttggctttcttttcttcctaaagtatcctgacttcttttttatttgttggtgattaagagctgttacgttttaattgaataagGATGAATCTGTTCGTTTGTGGAATGTTGAAACTGGGATATGTATTTTGATATTTGCTGGAGCTGGAGGTCATCGCTATGAAGTTCTAAGTGTG

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|71864778|gb|DT013833.1|DT013833
EST:     AAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAA                         GATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
genomic: AAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAAgtaggtgtca ... aatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
EST: gi|161719190|gb|FC065436.1|FC065436
EST:     AAATCAGGACTCAGGCACTGAAACCATCACTTGTGGTGTCTGCAAGCAAA                         GATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
genomic: AAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAAgtaggtgtca ... aatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
EST: gi|351053554|gb|FQ459301.1|FQ459301
EST:     AAATCAGGACTCAGGCACTGAGACCATCAATTGTGGTGTCTGCAAGCAAA                         GATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
genomic: AAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAAgtaggtgtca ... aatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
EST: gi|351036699|gb|FQ457412.1|FQ457412
EST:     AAATCAGGACTCAGGCACTGAGACCATCAATTGTGGTGTCTGCAAGCAAA                         GATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
genomic: AAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAAgtaggtgtca ... aatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
EST: gi|351043856|gb|FQ452650.1|FQ452650
EST:     AAATCAGGACTCAGGCACTGAGACCATCAATTGAGGTGTCTGCAAGCAAA                         GATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
genomic: AAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAAgtaggtgtca ... aatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
EST: gi|352791431|gb|FQ481010.1|FQ481010
EST:     AAATCAGGACTCAGGCACTGAGACCATCAATTGTGGTGTCTGCAAGCAAA                         GATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
genomic: AAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAAgtaggtgtca ... aatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
EST: gi|161711022|gb|FC059448.1|FC059448
EST:     AAATCAGGACTCAGGCACTGAAACCATCACTTGTGGTGTCTGCAAGCAAA                         GATGAGTCAGTGCGGTTATGGAAT
genomic: AAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAAgtaggtgtca ... aatcaaccagGATGAGTCAGTGCGGTTATGGAAT
EST: gi|294965480|gb|GW839051.1|GW839051
EST:     AAATCAGGACTCAGGCACTGAGACCATCAATTGTGGTGTCTGCAAGCAAA                         GATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
genomic: AAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAAgtaggtgtca ... aatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
EST: gi|351033874|gb|FQ447912.1|FQ447912
EST:     AAATCAGGACTCAGGCACTGAGACCATCAATTGTGGTGTCTGCAAGCAAA                         GATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA
genomic: AAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAAgtaggtgtca ... aatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaagtttttaatttataatggtggttaaatctacggaaaaaaaatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATATTTTCTGGAGCTGGGGGTCATCGCAATGAAGTCTTGAGTGTG
        ttttaat  putative branch site (score: 3)
     agtttttaatttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtgtcagatatttttttaaagtttttaatttataatggtggttaaatctacggaaaaaaaatcaaccagGATGAGTCAGTGCGGTTATGGAATGTTCACACGGGAATATGCATTTTGATATTTTCTGGAGCTGGGGGTCATCGCAATGAAGTCTTGAGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT