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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgttggtttgatcactaaatttatttctaacagtgaaggagtatattttaagatttatcagtattcggaaataaaatagggaatcccctggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTAACCTTGGAAGAACTGCGCCAATTGTCTGATGATACAAACACATACAAGT

Basic information

species Vitis vinifera
transcript Vv11s0065g00480.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g26440.1 (Oryza sativa), 3'ss of exon 2
cttgttggtttgatcactaaatttatttctaacag---tgaaggagtatattttaagatttatcagtattcggaaataaaatagggaatcccctggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTAACCTTGGAAGAACTGCGCCAATTGTCTGATGATACAAACACATACAAGT
 | |  | ||   |||  || ||  ||  ||||     | | |||    |    |   || |    ||  |   |||| || |  |       |  ||  ||| |||| |  ||||||||    ||||| || |||||||||||||||| | | ||  |||| ||||| ||||||||| | ||| |||||||||| |||||| 
-tggaagtttctttcaggaatttccttcgtaacgcatctcatggatgccaaagcattgttgacacataacctctaatataacaatgctgtttttttat--cagTTGCAAACTCAGATGCGCTCTAAAGAGGGTGAAAAGAAGCGTGCTTACCTCACACTGGAGGAACTTCGCCAATTGCCAGATAATACAAACACTTACAAGA

upper sequence: Vv11s0065g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G135691_T02 (Zea mays), 3'ss of exon 2
cttgttggtttgatcactaaatttatttctaac---agtgaaggagtatattttaagatttatca-gtattcggaaataaaatagggaatcccctggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTAACCTTGGAAGAACTGCGCCAATTGTCTGATGATACAAACACATACAAGT
 || |   ||||||    ||  || ||| |||    | |     ||||  || ||   | | |||   |  |     |  ||||     |  | |  ||  ||| | || | ||| |||||    |||||||| |||||||||||||| | | | || ||||| ||||| ||||| ||| | |||||||| ||||| |||||| 
attttacctttgatgg--aagcttctttgtaaggaaatttctatagtaacttctagcctatgtcatagaacctctgttgcaataatacctttctttcat--cagTTACAAACCCAAATGCGTTCTAAAGAAGGGGAAAAGAAGCGTGCCTACCTTACTTTGGAGGAACTTCGCCAGTTGCCAGATGATACCAACACCTACAAGA

upper sequence: Vv11s0065g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G37640.1 (Glycine max), 3'ss of exon 2
-cttgttggtttgatcactaaatttatttctaacagtgaaggagtatattttaagatttatcagtattcggaaataaaatagggaatcccctggat--ttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTAACCTTGGAAGAACTGCGCCAATTGTCTGATGATACAAACACATACAAGT
 |    | ||  ||| |      || ||  |     ||  |  |  | ||    | |   | ||  |   |  ||  | ||     |||| |||    | |||||||| | |||||||||   |||||||| ||||||||||||||||||  | ||| |||| || |||   ||| |  |||||||||| ||    ||||| |
cccacctagtgggataa--ggcgttgttgttgttgttgttgttgcttgttaggggttgcctgagactcttgggattta-tattatctcccttggcacatgcagGTGCAAACCCAGATGCGTTCCAAAGAAGCAGAAAAGAAGCGTGCTTTTCTGACCATGGAGGAGCTGAAGCAAGTTCCTGATGATACTAATGTTTACAAAT

upper sequence: Vv11s0065g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G07340.1 (Arabidopsis thaliana), 3'ss of exon 2
cttgttggtttgatcactaaatttatttctaacagtgaaggagtatattttaagatttatcagtattcggaaata-aaatagggaatcccctggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTAACCTTGGAAGAACTGCGCCAATTGTCTGATGATACAAACACATACAAGT
| |  |    || |   |||    |    |  |  |    |  ||| | | | |   |      |  | |||||   |||  |||      |    |  |||||||||| |||||||| |||||||| ||||| |  ||||| ||||||||||||||||| || ||| | | |||| |||| || |||||||| |||||||
ccttctttcatgttgtgtaatgacaaaattggctttcctaggttat-tgtcatgtggtgctgaaaaactgaaatgtgaatgtggatgggttttatatatagGTGCAGAATCAGATGCGCAACAAAGAGGGAGATAGAAAGCGAGCTTTCTTAACCTTGGAGGAGCTGAGGCCATTGCCTGAAGAGACAAACACCTACAAGT

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|110396623|gb|EC962315.1|EC962315
EST:     TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAG                         GTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
genomic: TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAGgtgagtgctt ... tggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
EST: gi|71873337|gb|DT022392.1|DT022392
EST:     TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAG                         GTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
genomic: TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAGgtgagtgctt ... tggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
EST: gi|110380311|gb|EC945566.1|EC945566
EST:     TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAG                         GTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
genomic: TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAGgtgagtgctt ... tggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
EST: gi|110421110|gb|EC987398.1|EC987398
EST:     TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAG                         GTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
genomic: TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAGgtgagtgctt ... tggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
EST: gi|110390962|gb|EC955912.1|EC955912
EST:     TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAG                         GTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
genomic: TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAGgtgagtgctt ... tggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
EST: gi|110428276|gb|EC994743.1|EC994743
EST:     ATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAG                         GTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
genomic: ATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAGgtgagtgctt ... tggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
EST: gi|110392562|gb|EC958071.1|EC958071
EST:     TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAG                         GTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
genomic: TTATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAGgtgagtgctt ... tggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
EST: gi|110414808|gb|EC980666.1|EC980666
EST:     ATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAG                         GTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA
genomic: ATGGAGATTCAAGGTCACATGATCGAAACTACTGGAAAATTGAAGCAGgtgagtgctt ... tggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttaagatttatcagtattcggaaataaaatagggaatcccctggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTAACCTTGGAAGAACTGCGCCAATTGTCTGATGATACAAACACATACAAGT
                                        tcccct  CT-rich tract
                         aaataaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgttggtttgatcactaaatttatttctaacagtgaaggagtatattttaagatttatcagtattcggaaataaaatagggaatcccctggatttcagGTGCAGAACCAGATGCGGAACAAAGAAGGAGAAAAGAAGCGTGCTTTCTTAACCTTGGAAGAACTGCGCCAATTGTCTGATGATACAAACACATACAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
cttgttg
- - - - - - - cactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa