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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaacccgaggttctttgagtcagatctggtgagaatttcttttccttcaggtcagaattatgacccttttatgaagccagaattcatttttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCACTGGCTGTTCAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACT

Basic information

species Vitis vinifera
transcript Vv08s0007g05350.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g46520.1 (Oryza sativa), 3'ss of exon 2
aaaaacccgaggttctttgagtcagatct-ggtgagaatttcttttccttcaggtcagaattatgacccttttatgaagccagaattcatttttat---tgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCACTGGCTGTTCAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACT
         |  ||||  || ||| || |     | | || | |||| |     ||| | ||||      |  ||| | | | ||| | | |  ||   | ||| |||||| ||||||| || |||||||||||  | ||||| |||| ||| ||||| || ||||||   |||||||||||||||||||| || |||||||| 
--gttgttcacattcta-gattcatatttcaaccatatttacctttcttatccttcaaatttatctgagctgcatgga-ctaaaatgcttctcaatatatccagGTATGTGGATGATGGTAGGCCCTTCTGGCAGCATATAGTTAGCTCTTCAACTGGATGCTCAGATTTACAGTACTTTGAGGAACTTTATCAGTACTATACA

upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g24070.1 (Oryza sativa), 3'ss of exon 2
aaaaacccgaggttctttgagtcagatctggtgagaatttcttttccttcaggtcagaattatgacccttttatgaagccagaattcatttttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCACTGGCTGTTCAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACT---------
                                                                                           ||  |  || |||||| ||||||| |||||||| |||||  | |||||||  | ||| |||||||||||||||   ||||||||||||||||| || || |||||||           
-------------------------------------------------------------------------------------------ttggttaaggtatgtggatgatggtagacccttttggcagcatatagtcacttcttctactggctgttcagatttgcagtactttgaggaactatatcagTACTATATGACAGAGAAG

upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G898740_T02 (Zea mays), 3'ss of exon 1
aaaaacccgaggttc-tttgagtcagatctggtg----agaatttcttttccttcaggtcagaattatgacccttt--tatgaagccagaattcatttttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCACTGGCTGTTCAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACT
     || ||  ||  | |     |  | |  |     |||||  |||||  |  |  | |  ||| |  |  ||   ||| |||  |  || |     |    ||| |||||| ||||||| ||| |||| |||||  |||||||||  | ||| || || ||||||||| | ||||||||||||||||| || || |||| ||  
-----cctgatatttatctcgactatctttttttttctagaatgcctttttatata--ttatcattgttccatttcgatattaagttactataccaacattgaccagGTATGTGGATGATGGGAGAACCTTTTGGCAGCACATAGTCACTTCTTCTACAGGATGTTCAGATGCACAGTACTTTGAGGAACTCTATCAATACTTTATG

upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G31340.1 (Glycine max), 3'ss of exon 2
-----aaaaacccgaggttctttgagtcagatctggtgagaattt-cttttccttcaggtcagaattatgacccttttatgaagccagaattcatttttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCACTGGCTGTTCAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACT
     |||||    |   ||||      || | | | |  | ||  ||  |  |     | ||  | || |   || | ||         ||| ||| |||||||||||||| |||||||| || || || |||||||||||||| || | ||||||||||||||||||| |||| || ||||| ||||||||  |||| ||||| 
aaataaaaaaaagtaatctcttacgaatagctgtagaggtacttcactgcttttattatttagtgtaattaagattctttgttt------ttcttttatattgcagATATGTTAATGATGGTAGGCCTTTTTGGCAATACATAGTTAGTTATTCCACTGGCTGTTCAGATCCTCAATATTTTGAAGAACTTTATAACTATTATACA

upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G28600.1 (Glycine max), 3'ss of exon 2
--aaaaacccgaggt--tctttgagtcagatctggtgagaatttcttttccttcaggtcagaattatgacccttttatgaagccagaattcatttt-tattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCACTGGCTGTTCAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACT
  || ||    | ||  ||| | |  || | |||  ||||   | |  | |||   |||||| |||  |   ||  | ||  ||    ||  ||||  ||||||||||||| |||||||| || ||||| |||||||||||||| || | ||| |||||||| |||||| |||| |||||||| ||||||||  |||| ||||| 
taaataaaaaaaagtaatctcttacacatagctgtagagacactatactgctt---gtcagatttagtataatt--aagattcctttttttcttttacattgcagATATGTTAATGATGGTAGGCCCTTTTGGCAATACATAGTTAGTTATTCTACTGGCTGCTCAGATCCTCAATACTTTGAAGAACTTTATAACTATTATACG

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|32267815|gb|CD716974.1|CD716974
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|110731628|gb|EE106216.1|EE106216
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|30299817|gb|CB976611.1|CB976611
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|110395612|gb|EC961279.1|EC961279
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|110429697|gb|EC996199.1|EC996199
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|22014482|gb|BQ799516.1|BQ799516
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|161719017|gb|FC067637.1|FC067637
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAC                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|26258618|gb|CA809681.1|CA809681
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|33403871|gb|CF209498.1|CF209498
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|22011451|gb|BQ796485.1|BQ796485
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|71871882|gb|DT020937.1|DT020937
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|110725316|gb|EE101677.1|EE101677
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|161712968|gb|FC062094.1|FC062094
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|110730112|gb|EE106820.1|EE106820
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|110713079|gb|EE088696.1|EE088696
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|71877278|gb|DT026333.1|DT026333
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|26266814|gb|CA817877.1|CA817877
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|294965827|gb|GW837310.1|GW837310
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|34320237|gb|CF372991.1|CF372991
EST:     ATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCT-GCAATACATAGTCAGCTTTTCCNC
genomic: ATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|26257149|gb|CA808212.1|CA808212
EST:     ACAGATACAGAAGGGCTTATGCACAGCCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: ACAGATACAGAAGGGCTTATGCACAGCCC-TGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|110731791|gb|EE106512.1|EE106512
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|110688614|gb|EE067366.1|EE067366
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|294966056|gb|GW837423.1|GW837423
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|22014205|gb|BQ799239.1|BQ799239
EST:     AAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|110713855|gb|EE090151.1|EE090151
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAA                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|71877965|gb|DT027020.1|DT027020
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|161715593|gb|FC068349.1|FC068349
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
EST: gi|110712773|gb|EE088110.1|EE088110
EST:     AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAG                         ATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC
genomic: AACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTCGACTCAGgtgattttaa ... tttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcaggtcagaattatgacccttttatgaagccagaattcatttttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCACTGGCTGTTCAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACT
                                       ttcattttt  CT-rich tract
                                   agaattcatttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaacccgaggttctttgagtcagatctggtgagaatttcttttccttcaggtcagaattatgacccttttatgaagccagaattcatttttattgcagATATGTGAATGATGGAAGACCCTTCTGGCAATACATAGTCAGCTTTTCCACTGGCTGTTCAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
aaaaacc
- - - - - - - - - - - - - -ctggtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagcca