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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgtttcaacccaaacctggcttctagatttgctcagctagttggaatgtcatcctcctgtactaattatcttcgtatttttatagcacaggaacaaaaggacatcttgaattcctactacatttacaatttaatcaagttgaacttatgttgtacatctgcatgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTTTGAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCT

Basic information

species Vitis vinifera
transcript Vv06s0080g00560.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g33080.1 (Oryza sativa), 3'ss of exon 3
gtaaatgtttcaacccaaacctggcttctagatttgctcagctagttggaatgtcatcctcctgtactaattatcttcgtatttttatagcacaggaacaaaaggacatcttgaattcctactacatttacaatttaatcaagttgaacttatgttgtacatctgcatgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTTTGAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCT
                                                    ||   | | |   | || ||        ||| || |    |||||    |    ||   || ||   | |||  | |  | ||  |||        | |||| |  |    | | || |    ||| | |||||||||||||| ||| ||| ||| || ||||| || ||||| ||||| ||||| |||||||| |||||||||||| | |||||  ||||||||
----------------------------------------------------gtaggcttgcctcattacttg-------attcttgt----caggagtccacaagcaa--tgtatatgttctatttctgtagtt--atc--------cctatgcttcattctttcttgttcgatagGTTTCAAAAACTTGCAAAGGAGCTGGAAGTTGTAATACCTGTCAGCTTTTTTGAGGAGGCGAACAATGCACATTACAATTCAGTAGCCATTATTGATGCT

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G31100.2 (Glycine max), 3'ss of exon 4
gtaaatgtttcaacccaaacctggcttcta-gatttgctcagctagttggaatgt-catcctcctgtactaattatcttcgtatttttatagcaca-ggaacaaaaggac--atcttgaattcctactacatttacaatttaatcaagttgaacttatg-ttgtacatctgcatgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTTTGAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCT
|||||    |  |   |||  | ||||||   || ||||    ||||       | ||| |  ||  |  || |     |||||| |  |     | ||  || | | ||  || |||  ||  |  |  || | ||   |  |  | |  | |||||  ||||     ||      |||||| ||||| ||||||||||||||||| || ||||| |||||||||||||||||||| |||||||||||||| ||||| |||||||| |||||| ||||| ||
gtaaaataattga---aaaagtagcttctgtaatctgcttc-ttagtcactgcttgcatgccactcaatgaactggaaccgtattatggtgttttaaggggcagaggaacaaatattggcttagtcttttatgtgcatcatcctgtaatgaatcttattcttgtttcaatgttcatgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTTTGAGGAGGCAAACAATGCACATTATAATTCAATAGCCATAATTGATTCT

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G39210.1 (Glycine max), 3'ss of exon 3
gtaaatgtttcaacccaaacctggcttctagatttgctcagctagttggaatgtcatcctcctgtactaattatcttcgt----atttttatagcacaggaacaaaaggacatcttgaattcctactacattt-acaatttaatcaagttgaacttatgttgtacatctgcatgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTTTGAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCT
                                     | |  || ||| ||    | | || |||| |     |||| ||      ||  ||  |||   |   |  ||| | | |    | || ||  |    ||| |  || ||  ||   |||   || |  || | ||||  |||||| ||||| ||||||||||||||||| || ||||| ||||||||||||||||| || |||||||||||||| ||||| |||||||  |||||| ||||||||
------------------------------------gtaaaataattgaaaaagtagcttc-tgtaatctgcttcttagtcactgcttgcatgccactcaatggactgga-accatattatgctgctgtaagggacagtggaaccatattattctt---ttttgaatgttcatg--atgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTTCGAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCT

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 3
gtaaatgtttcaacccaaacctggcttctagatt----tgctcagctagttggaatgtcatcctcc-tgtacta--attatcttcgtatttttatagcacaggaacaaaaggacatcttgaattcctactacatttacaatttaatcaagttgaacttatg-ttgtacatctgcatgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTTTGAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCT
|||||      ||   |||  |||||||| |  |    | |||||  | ||      |  |  ||  || ||||  |  || |  |  ||  | |   |  || | | ||  | || |||  ||  |  |  ||   ||   |  |  |||  | |||||  ||||     ||      ||| |||||||| ||||||||||||||||| || ||||| || ||||||||||||||||| |||||||||||||| ||||| || ||||| |||||| ||||||||
gtaaaa----taattgaaaagtggcttctgggatctacttctcagtcacttcttgcatgcttttcaatggactacaaccatataag-gttgctgtttaaggggcagagaaacaaatattggctttgtcttttatgctcatcatcctgtagtgaatcttattcttgtttcaatgttcataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTTTGAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCT

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaaatgtttcaacccaaacctggcttctagatttgctcagctagttggaatgtcatcctcctgtactaattatcttcgtatttttatagcacaggaacaaaaggacatcttgaattcctactacatttacaatttaatcaagttgaacttatgttgtacatctgcatgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTTTGAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCT
                                                              |||   | |  |  ||  |||| ||  |||       |||  |  |||| ||  |        || ||| || || |    || ||     |||| |    |  ||   |  ||||||||| || || ||||| || ||||| ||||||||||| ||||| |||||||| |||||||| | ||| ||||||||||| ||||| ||| ||||||||
-------------------------------------------------------------gtgtgacattgcttatccgatttctaacgca-----gtaaagtggaatctcgatgtatc----tatgtactatctagt--gttttaatg---gttggatggtttaatttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTTTGAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCT

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|294965150|gb|GW836981.1|GW836981
EST:     GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|71863030|gb|DT012085.1|DT012085
EST:     GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|71859592|gb|DT008647.1|DT008647
EST:     GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|71864994|gb|DT014049.1|DT014049
EST:     GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|294963940|gb|GW836815.1|GW836815
EST:     GATTTCTTTCAGCGAGCAAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|26257496|gb|CA808559.1|CA808559
EST:     GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|71863516|gb|DT012571.1|DT012571
EST:     GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|110385570|gb|EC950109.1|EC950109
EST:     A-TTCTTTCAGCGAGCTAAGCC-TACAAGGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: ATTTCTTTCAGCGAGCTAAGCCTTACAA-GGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|352782096|gb|FQ469394.1|FQ469394
EST:     GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|71865063|gb|DT014118.1|DT014118
EST:     GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|71858886|gb|DT007941.1|DT007941
EST:     GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
EST: gi|18459688|gb|BM437966.1|BM437966
EST:     GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG                         GATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT
genomic: GATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgttt ... tgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatttacaatttaatcaagttgaacttatgttgtacatctgcatgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTTTGAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCT
          atttaat  putative branch site (score: 4)
     ttacaatttaatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgtttcaacccaaacctggcttctagatttgctcagctagttggaatgtcatcctcctgtactaattatcttcgtatttttatagcacaggaacaaaaggacatcttgaattcctactacatttacaatttaatcaagttgaacttatgttgtacatctgcatgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTTTGAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG