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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtattgctttaccgaggttctatgcatcatgctagctatatttcatctggaccgccaaactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG

Basic information

species Vitis vinifera
transcript Vv08s0007g02300.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g01350.1 (Oryza sativa), 3'ss of exon 4
-----------gtctgtattgct-ttaccgaggttctatgcatcatgctagctatatttcatctggaccgccaaactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG
            | |  |  ||  ||      | |   || |  ||  |   ||| | ||||||       |      ||| | ||      |     |  |||  ||||||||||| ||||  |||||||||||||| |||   ||||| |||||||||||||| ||||| |||||  | || || ||  |||||||||| |
tttaagtgcggttatcaaccgcccttgaaattgcttgttggactatcttgagtat-tatcatctt--ttttcgcgtaaaacgaatgccctgatccacctgtagAATATGCAAGATGAAATGACTGACCTGATGGATGTGAGCAACGAAATACAAGAATCCCTTGGTAGAAGCTACAACATCCCTGACGATGTTGATGAGGAAG

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g01250.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------gtctgtattgctttaccgaggttctatgcatcatgctagctatatttcatctg-gaccgcc----aaactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG
                                             | |  ||  || |   || | |  |     | |  | | | ||   | |   |  ||     || ||  ||   || || || || | | |||||| ||||||| ||||||||||| || |||||||| |||   ||||| || ||| | || || ||||| |||||||| || ||||||||||| ||||| |
gtacgcagcatctttttgtgtaacatattcgtcatgttttcaagattttctggcttgcaatggattttcgttgtttccctgttttcttctgtttccaattgcatctgaatctagacccatgctt-ttcttatctgcagAGCTTGCAAGACGAGATGATGGATCTTATGGATGTGAGCAATGAAATACAGGAAACTCTCGGAAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAG

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G092468_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------gtctgtattgctttaccgaggttctatgcatcatgctagctatatttcatctggaccgcca----aactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG
                                                    || | |||| |            | | ||   || |   ||| || | | | ||  |       | |||||||  |   |  | |  |    |||| |||||||||||||||||||| || |||||||| ||| | ||||| |||||| | ||||||||||| ||||| || ||||||||||| |||||||| |
gtatgttattaagcattctcccatctttactctcaccagattcctcgcgctttcagcattgatgccttacatgcatttacactttgttgcttattttcctttttgattgatgttgcatctgaacatatacctcctatgatccatagAGTATGCAAGATGAGATGATGGATCTTATGGATGTGAGCACTGAAATACAAGAAACTCTTGGCAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAG

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G33960.1 (Glycine max), 3'ss of exon 4
gtctgtattgctttaccgaggttctat-gcatcatgctagctatatttcatctggaccgccaaactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG
|| |||||  |||| |     |  ||| || ||   |||     |     | |  |        || |||   ||||   |  | | |  ||| | |||||||||||||||||||||| |||||||||||    |||||||||||  |  | || ||||| || |||||||| ||||||||||| |||||||
gtatgtatctctttccttttctcttatagcttctatctaaagtgaaaatttttaaaaattttgtcttaactgttgatccatgctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATG

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 4
gtctgtattgctttaccgaggttctatgcatcatgctagcta-tatttcatctggaccgccaaa-ctgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG
|| |||||| | || ||     ||| |  | | | ||| ||| | |   |||   |     |   || |||   ||||   |  | |    ||| | |||||||||||||||||||||| |||||||||||    ||||| |||||  |  | || ||||| || |||||||| |||||||||||||||||||
gtatgtattccctttccttttctct-tatagctt-ctatctaatctaatatcaaaatttttacgtcttaactgttgatccatgctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGATGAGGATG

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G10640.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------gtctgtattgctttaccgaggttcta---tgcatcatgctagctatatttcatctggaccgccaaactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG
              |   |  |   | |  |||| ||   ||  ||| |||   | | |   || ||    |||  |    || |   |||| |  |     ||||   | ||||| ||||||||||| ||||||||||| || || |||||||||||||| ||||| || || |||||| | || |||| | |||| |||||||
gtacgttgttaagttacttaacaacatcttggttttatcttgtttcaagctt-ttctctggtatttgatttgcctgatactacgatctattgatggta----cagAATTTACAAGACGAGATGATGGATCTGATGGATGTTAGTTCTGAAATTCAAGAATCACTTGGTAGGAGCTACAATATTCCTGATGGCCTTGACGAGGATG

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 4
gtctgtattgctttaccgaggttctatgcatcatgctagctatatttcatctggaccgccaaactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG
    ||||  |||        ||| |       |  |   | |  ||| |    || |      | || || |  ||||| |      ||||   |||||||||| ||||||||| | |||||||  || || |||||||||||  | ||||| || || |||||||| || ||||||||||| || ||||
----gtatgtcttggttcttattcaagcttctcttgtgtgtttgcttcctagatactgttttggttaagaattatttgttgtataccacagAATTTGCAAGATGATATGATGGACTTAATGGATGAGAGTTCTGAAATTCAAGAGACACTTGGTAGGAGCTACAATGTTCCTGATGACATTGACGAAGATG

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|110688527|gb|EE067183.1|EE067183
EST:     ACAAGGATTTGAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGAT                         AGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
genomic: ACAAGGAGTTAAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGATgtctgtattg ... ttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
EST: gi|33404120|gb|CF209747.1|CF209747
EST:     ACAAGGATTTGAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGAT                         AGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
genomic: ACAAGGAGTTAAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGATgtctgtattg ... ttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
EST: gi|110686349|gb|EE063885.1|EE063885
EST:     ACAAGGATTTGAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGAT                         AGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
genomic: ACAAGGAGTTAAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGATgtctgtattg ... ttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
EST: gi|110690195|gb|EE067084.1|EE067084
EST:     ACAAGGATTTGAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGAT                         AGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
genomic: ACAAGGAGTTAAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGATgtctgtattg ... ttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
EST: gi|71859039|gb|DT008094.1|DT008094
EST:     ACAAGGATTTGAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGAT                         AGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
genomic: ACAAGGAGTTAAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGATgtctgtattg ... ttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
EST: gi|71868774|gb|DT017829.1|DT017829
EST:     ACAAGGATTTGAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGAT                         AGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA
genomic: ACAAGGAGTTAAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGATgtctgtattg ... ttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctatatttcatctggaccgccaaactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG
                                 aactgat  putative branch site (score: 3)
                                       ttgtttttgttttc  CT-rich tract
                                      attgtttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtattgctttaccgaggttctatgcatcatgctagctatatttcatctggaccgccaaactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG