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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagaaatccgatagatttctaactgactttttccactcctgtatcttaacatgttagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG

Basic information

species Vitis vinifera
transcript Vv11s0016g00700.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 4
----------------------------------gtaagtagaaatccgatagatttctaactgactttttccactcctgtatcttaacatgtta-gtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG
                                   ||| |   |||    |   ||||    | || |||||||    | |  ||||  ||  ||  ||  ||||||||| |||||||| ||||| |||||||||||||| |||| ||| ||||||||||||||||
gtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacatttt--cttatgatcctacattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 4
gtaagtagaaa----------tccgatagatttctaa---ctgactttttccactcctgtatcttaacatgttagtt------------tgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG
|||||   |||          || | ||| ||  | |    | | | | |    |  | |  |  || |   |  ||            | ||| ||||| ||||  |||| |||||||||||||||||||||| | ||||| ||||| ||| |||
gtaagagaaaagctattcatttctgctagtttgttgaagcttaattatgtttttttttctccccaaaaacactcattgaagaaaaatgatacagTTTTGGGCAGCTTATCAGAGTTAATTGGGCATATGCTAGTGGGCAGAGGGAGGACACAACAG

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 4
----------------------------gtaagtagaaatccgatagatttctaactgacttt--ttccactcctgtatcttaacat-gttagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG
                            |  ||||         |    ||   | || | ||  ||   |||   | | |||| |     |   | ||||| ||||||||| || ||||| |||||||||||| | |||| || ||| ||||| |||||||
aaaagccaaaattacttacagttcaaaagggagtacgtgctaattcctcttaacattgcccttgttttggctctgattttttaataccaccaaaattcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 4
gtaagtagaaatccgat--agatttctaac-tgactttttccactcctgtatcttaacatgt------tagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG
||| || |||  |  ||   || || |      ||||||   | |    ||| ||||||         | || ||||| ||||| ||||| || || ||||| ||||| |||||||| || |||||||||||||| ||||
gtatgtggaatcctaattttgagttatggtacaacttttattaatttaatattttaacacacaccacattgtctgcagTTTTGGGCAGCCTATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAG

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 5
gtaagtagaaatccgat--agatttctaac-tgactttttccactcctgtatcttaacatgtta-------gtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG
||| || |||     ||   ||||| |      ||||||   | |    ||| | ||||    |       || | ||| ||||| ||||| || || ||||| ||||| |||||||| || |||||||||||||| ||||
gtatgtggaatcttaattttgatttatggtacaacttttattaatttaatatttaaacacaacaacacattgtctacagTTTTGGGCAGCCTATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAG

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
------------------------------------gtaagtagaaatccgatagatttctaactgactttttccactcctgtatcttaacatgttagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG
                                    | | | |   | |  ||||||     | | | || ||   ||  | |   |    ||| |  | || || ||||| ||||| ||||||||||||||||||||||| ||  | ||||||||||||||  |||
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagat-----agtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S84_51V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------gtaagtagaaatccgatagatttctaactgactttttccactcctgtatcttaacatgttagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG
                                 | ||   ||| ||  || |||||  || |    |    || ||    ||  |   | | |  ||||||||||||| ||  | |||||||| |||||||||||||| ||  | || |||||||||||| |||
tggtcgcaaatagttttaaaacgataaaacgacgaaatccgaattcttatggattttgaaattggctgg--cattctcaaatactctgaggctgatttgcagGTTTGGGCAATCTATCAAAGTAAATTGGGCATATGCGAGCGGACAAAGAGAGGATACAACAG

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|110685954|gb|EE063126.1|EE063126
EST:     GACCGGAGATCTGCTGCCCTTTCTATTGTGACTCTGAATGGAAGGCATCT                         GTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGA
genomic: GACCGGAGATCTGCTGCCCTTTCTATTGTGACTCTGAATGGAAGGCATCTgtaagtagaa ... tagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGA
EST: gi|110728255|gb|EE103663.1|EE103663
EST:     GACCGGAGATCTGCTGCCCTTTCTATTGTGACTCTGAATGGAAGGCATCT                         GTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGA
genomic: GACCGGAGATCTGCTGCCCTTTCTATTGTGACTCTGAATGGAAGGCATCTgtaagtagaa ... tagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGA
EST: gi|156737274|gb|EV241395.1|EV241395
EST:     GACCGGAGATCTGCTGCCCTTTCTATTGTGACTCTGAATGGAAGGCATCT                         GTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGA
genomic: GACCGGAGATCTGCTGCCCTTTCTATTGTGACTCTGAATGGAAGGCATCTgtaagtagaa ... tagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGA
EST: gi|161705551|gb|FC057541.1|FC057541
EST:     GACCGGAGATCTGCTGCCC-TTCTATTGTGACTCTGAATGGAAGGCATCT                         GTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGA-AAA
genomic: GACCGGAGATCTGCTGCCCTTTCTATTGTGACTCTGAATGGAAGGCATCTgtaagtagaa ... tagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGA
EST: gi|294966632|gb|GW839623.1|GW839623
EST:     GACCGGAGATCTGCTGCCCTTTCTATTGTGACTCTGAATGGAAGGCATCT                         GTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCCGAGAGA
genomic: GACCGGAGATCTGCTGCCCTTTCTATTGTGACTCTGAATGGAAGGCATCTgtaagtagaa ... tagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagatttctaactgactttttccactcctgtatcttaacatgttagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG
     atttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagaaatccgatagatttctaactgactttttccactcctgtatcttaacatgttagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT