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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag

Basic information

species Vitis vinifera
transcript Vv06s0009g03520.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os05g36070.2 (Oryza sativa), 5'ss of exon 8
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag
   ||||| ||| | |||||||||||||||||||||||||||||||| |||||||||||||| ||||| || |||||||| || ||||| |||  |||               || ||       | ||| |||       | ||| |||||       | ||  ||||||  || |       || | |   ||| |   || ||    ||    ||||        
AGCGGACTCTTTTTCTATGATATTTTCTGGGTCTTCTTCACTCCAGTTATGGTCAGTGTTGCCAAGTCATTTGATGCTCCAATAAAGgtaagtattcc---------------ttgatttc----actcttgttgcaatagccattcatttc-------tatacctaatcaaaaaat-------acgtaaggtttccagtagttattttcgtctgtttct--------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os02g02530.3 (Oryza sativa), 5'ss of exon 7
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag
|| || || ||| | ||||||||||||||||| ||||||||||| || ||||||||||||||||| || || ||||| || || ||||| |||  ||    | |     ||| || |  || |          ||||| | |||  | | |   ||| ||   |  ||      | | |  ||  |    || ||||  ||                           
GCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAGgttagtgttctttataagt---gattttgactcttg----------ttttgatacaaaatgtctttttctttttacaaaaaaaggctaatctggttatccccttttttctgcatag-------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G150251_T01 (Zea mays), 5'ss of exon 8
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag
|  ||||||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| || || || || ||||||||||| ||||||||  |  |      |||||    ||  |  |  |||   | ||   |   ||| || | || | ||  || |  | | || | | | || |  |  | |    || |     ||   ||||                 
GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagc-actctttcatactgaacctttttttgttaataccattgtcagtcactcagtt-agttggttccatttttctca-tcttgatgcttcagctgatctggctttgtttggttatgtacag-----------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G044348_T04 (Zea mays), 5'ss of exon 8
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag
|  ||||||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| || || || ||||||||||| || |||||| ||    |    | |||||  |  |  || | | || |    ||||  |||      | |||  | || |  |  | |||       |   ||| |||  ||||    |                             
GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAGgtcggtggctctttcctactgaact--tggtctttgttaataccattttcagtt------agttccatatgcttcagctgatc-------tcgctttgcttggttatgtacag----------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA14G21190.1 (Glycine max), 5'ss of exon 3
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag
|| ||||| ||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||| || || |||||||| || ||||| |   ||     | || | |    || ||  |   |||  | || |   ||| || |  |||    ||       || ||    ||  |   |  ||||| || ||  |                              
GCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAGgttaac-attttaatgaaataat---tttatttttcctatcttcgtgtgaagtttaaat-gtttaatactccc----ttgattgcgaaact--gtagactttcttgtttaa------------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA04G08510.1 (Glycine max), 5'ss of exon 8
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatc-ctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag
|| || || ||||| ||||| ||||||||||| |||||||| |||||||||||||| |||||||| || || |||||||| || ||||| |||| |   | | |  ||| ||    ||  |||  | |  | || |    || ||||   | |   || |  ||    || |  || | ||||  |  |    ||||  ||| |  | |   ||||| |  ||||||||
GCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAGgttagtttttttgctaa--tgaaatggagatttctgtttgtctttgtgtgaattttaattgtgtacttactatgatatcagataaaaaaatgtaataaatct----attcctaatattgtca---ttcaaattattttgcag

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA06G08620.3 (Glycine max), 5'ss of exon 8
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttat-tattctaaatgtaataacagttcaattctttttgcag
|| || || ||||| ||||| ||||||||||| |||||||||||||||||||| || |||||||| || || |||||||| || ||||| |  | |   | | |  ||| ||    ||    | |  |||   | |   ||  | || | |   | |  | | || |     ||||   ||| || |  || |||||  ||| |  | |   ||||| |  ||||||||
GCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTTAGCGTTGCAAAATCATTTGATGCTCCAATAAAGgttaagttttttgctaa--tgaaatggagatttctgtttgtctttgtgtgaattttaattgtata--tttactatgat-atcagataagaaaaatgtaataaatctattcctaatattgtca---ttcaaattattttgcag

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 5'ss of exon 7
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag
|||||||| ||| | |||||||| |||||||| ||||| |||||||| ||||| |||||||| || |||||||||||||| |||||||| ||| |   |  |      | |    |  ||     |   || || |   ||    ||| |    | |   |||||   |||||       ||||  || |                                      
GCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAGgttagtaa---aaatgcctcaaaagtacacaccataccaaattgattctgatttgttcttagtcaatttttcagtaatc--tcattgttacatatttctttcag-------------------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: PP1S47_5V6.2 (Physcomitrella patens), 5'ss of exon 8
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgt-cagttatccaggtcaactgagatattaatcctggatattctg--gtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag
|||||||| ||  | || || || |||||||| |||||||| || || ||||| || || |||||||| ||||||||||| || ||||| |      ||   ||   |      |  ||  || ||     |  || ||  |    |  || ||  |     || ||| |  |||   ||||  |   ||                                         
GCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagccccttatctgtttcttcgtggatggtgcatggcaagctgtgttatgagagagctacttgacaacaatggaatgagacat---gtttcgtgagct-----------------------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag
|| || || || || ||||| || |||||||| ||||||||||| ||||||||||  ||||| |||||||| |||||||| || |||||  | | ||   ||  | ||    ||   ||    ||       |                                                                                               
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctctcagtgcaatg---catccttctctaatccctccatgcag-------------------------------------------------------------------------------------------

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|71877015|gb|DT026070.1|DT026070
EST:     TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG                         CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
genomic: TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatc ... ctttttgcagCTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
EST: gi|27579299|gb|CB001994.1|CB001994
EST:     TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG                         CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
genomic: TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatc ... ctttttgcagCTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
EST: gi|110391760|gb|EC956760.1|EC956760
EST:     TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG                         CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
genomic: TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatc ... ctttttgcagCTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
EST: gi|34364249|gb|CF405834.1|CF405834
EST:     GTGATGGTCAGTGTTGC-AAGTCCTTTGATGCTCCTATTAAG                         CTTTTGTTCCCAACAGCTGATTCTGCCCGGNCATTTTCCATGCTTGGACTT
genomic: GTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatc ... ctttttgcagCTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
EST: gi|110361505|gb|EC924984.1|EC924984
EST:     TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG                         CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
genomic: TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatc ... ctttttgcagCTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
EST: gi|77579348|gb|DV218502.1|DV218502
EST:     TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG                         CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
genomic: TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatc ... ctttttgcagCTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
EST: gi|161717568|gb|FC066896.1|FC066896
EST:     TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG                         CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
genomic: TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatc ... ctttttgcagCTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
EST: gi|110376904|gb|EC941978.1|EC941978
EST:     ACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTTGATGCTCCTATTAAG                         CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
genomic: ACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatc ... ctttttgcagCTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
EST: gi|110730433|gb|EE107509.1|EE107509
EST:     TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG                         CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
genomic: TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatc ... ctttttgcagCTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
EST: gi|71874644|gb|DT023699.1|DT023699
EST:     TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG                         CTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT
genomic: TCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatc ... ctttttgcagCTTTTGTTCCCAACAGCTGATTCTGCCCGGCCATTTTCCATGCTTGGACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG