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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcctatccatgcacctgcttcttctatgccatagttattttttggtttggtctcaacattcagacacttataaactgttcatattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG

Basic information

species Vitis vinifera
transcript Vv14s0060g01290.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 8
gttcctatccatgcacctgcttcttctatgccatagttattt--tttggtttggtct-caacattcagacacttataaactgttca-tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG
|||| | |  | || ||| || |      |  ||| |||| |   ||  ||||  ||  || ||  | | | | |  |  ||   |  ||||  |||| ||||| |||||||| ||  | |||||||||||| | |||||||| |||||||||||| | ||||||
gttcat-tatacgc-ccttctacacagtagtaatatttatgtaaattcttttgcactataagataaatatattcagcatttgaaaaacatttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G28890.2 (Glycine max), 3'ss of exon 8
gttc-ctatccatgcacctgcttcttctatgccatagttattttttggtttg-gtctcaacattcagacacttataaactgttca-tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG
||||  ||| ||  |  || |  | |   |   ||  ||||   ||  ||||  |   || ||  | | | | |  |  ||   |  ||||  |||| ||||| |||||||| ||  |||||||||||||| | |||||||| ||||| |||||| | ||||||
gttcattatacactcttctacaccgta-gtaatatttttataaattattttgcattataagataaatatattcaacatttgaaaaacatttgtcagATTTCAAGGATGACCCCGACCTCTATGTTTTCCCCAACTTGAAGTACGTGGGGATTGAATTGTGGCAG

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------gttcctatccatgcacctgcttcttctatgccatagttatttttt----ggtttggtctc-aacattcagacacttataaactgttcatattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG
                                                     |   |||  ||| | | |     | |||   |   || || |||    |   |  | ||  | |   ||  | |   |   | |  || |   ||||| ||||| |||||||||||  ||||||| |||||| | ||||||||||| ||  ||||  | ||||||
gtaatttaggaatccgtatttatattcacctgaaatagagtttgagattctgatagttatggatgtaacagtagtatttattgtaagatttttgtttccctgagataatatctgataagtagtaagtctaagtatatcaatttgacacagAATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG

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|33401772|gb|CF207399.1|CF207399
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|110381806|gb|EC935430.1|EC935430
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|351056636|gb|FQ443263.1|FQ443263
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|349816036|gb|FQ413550.1|FQ413550
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|351027478|gb|FQ444727.1|FQ444727
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|110700083|gb|EE077719.1|EE077719
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAAAGATCTATGTTTTCCCCGATTTGA-GTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|349808465|gb|FQ405609.1|FQ405609
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|352794106|gb|FQ479348.1|FQ479348
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|349826885|gb|FQ418976.1|FQ418976
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|29781779|gb|CB346544.2|CB346544
EST:     GAATCCCAACTACAAGGGGAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|33401998|gb|CF207625.1|CF207625
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAACGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|110687446|gb|EE064865.1|EE064865
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|351043138|gb|FQ451311.1|FQ451311
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|351022735|gb|FQ428644.1|FQ428644
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|33402080|gb|CF207707.1|CF207707
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAACGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|77578221|gb|DV217893.1|DV217893
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|110708716|gb|EE086573.1|EE086573
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|161716555|gb|FC065240.1|FC065240
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTT-CCCCGATTTGAA-TATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|71870544|gb|DT019599.1|DT019599
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCC-GATTTGA-GTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
EST: gi|349810157|gb|FQ401603.1|FQ401603
EST:     GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG                         AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG
genomic: GAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatcc ... tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttggtttggtctcaacattcagacacttataaactgttcatattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG
                               ttataaactgttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcctatccatgcacctgcttcttctatgccatagttattttttggtttggtctcaacattcagacacttataaactgttcatattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG