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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGAGAGATCAAAGGAGGAAAAAAATAATTGCAGGAAATGGGATCTGGTACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgtctttttccactcttccacttttaccaatttctccaaacccctaaaaaaatattgagtgaaaatgaatcacttctctgagttctctcacgc...

Basic information

species Vitis vinifera
transcript Vv17s0000g05990.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA06G20570.2 (Glycine max), 5'ss of exon 1
GTAGAGAGATCAAAGGAGGAAAAAAATAATTGCAGGAAATGGGATCT------GGTACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttc-gtctttttccactcttccacttttaccaatttctccaaacccctaaaaaaatattgagtgaaaatgaatcacttctctgagttctctcacgc
      || |  |   |   || |     ||  ||  |   |||||       ||  |||||| ||| ||||||||||| || |||||  ||||||||||||| |||||||||  |  |||| | ||| ||| |      |   || ||     ||   |||| || ||  | |||||| | |    |||| |   | |||| ||  
------AGTTTCATTCACTTAACACTCCTTTTAAGAGAGAAGGATCAAACATGGGAGCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttgctttttcctacttttctaacaaagcactttcctttcttccaaaaaaataaaataaaatgaaaaagcact-tttcttttgttgctcttacat

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA05G01160.1 (Glycine max), 5'ss of exon 1
GTAGAGAGATCAAAGGAGGAAAAAAAT--AATTGCAGGAAATGGGATCTGGTACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgtctttttccactcttccacttttaccaatttctccaaacccctaaaaaaatattgagtgaaaatgaatcacttctctgagttctctcacgc------------------------------------
  |   | |  ||     | |   | |  |         ||||||||||||  | || ||||| ||||||||| | ||||||||| | ||||| ||||| |||||||||  | |||||   || || | || || |   | |||| || | |     | | | |  |   ||  ||  ||  || |||   |  |||||                                       
--ACTAACACTAACACTAGCATTCACTCAAGAGATCAATAATGGGATCTGGGGCCGGCAATTTCCTCAAGGTGCTTCTCAAAAACTTCGATGTGCTTGCTGGgtatgttttttttttttttctttttccctcttccttctctctcaaatcac-----acattctccaa--aatgtgcttcctttttctctttcttctcaactgatatgttatgttatctatttttgtttctattgcag
















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|34544790|gb|CF513022.1|CF513022
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|351016143|gb|FQ435463.1|FQ435463
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATCGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|349825153|gb|FQ415700.1|FQ415700
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|349824511|gb|FQ413178.1|FQ413178
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|110696491|gb|EE072653.1|EE072653
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|71875506|gb|DT024561.1|DT024561
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|349825152|gb|FQ415699.1|FQ415699
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|351020210|gb|FQ445817.1|FQ445817
EST:     ACTGGAAATTTTCTCAATGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|351018684|gb|FQ424791.1|FQ424791
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|110424630|gb|EC990997.1|EC990997
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|349829195|gb|FQ419727.1|FQ419727
EST:     ACTGGAAATTTTCTCAATGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|294966237|gb|GW839460.1|GW839460
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|34549707|gb|CF517939.1|CF517939
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|110412973|gb|EC978742.1|EC978742
EST:     ACTGGAAATTTTCTCAAGGTGGGGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|349817530|gb|FQ407320.1|FQ407320
EST:     ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|110702147|gb|EE080527.1|EE080527
EST:     CTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: CTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT
EST: gi|349833130|gb|FQ416508.1|FQ416508
EST:     ACTAGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGG                         GCCTGTCGTTAGTCTTGCTTATCCTCT
genomic: ACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgt ... tgatttgcagGCCTGTCGTTAGTCTTGCTTATCCTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGAGAGATCAAAGGAGGAAAAAAATAATTGCAGGAAATGGGATCTGGTACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttcgtctttttccactcttccacttttaccaatttctccaaacccctaaaaaaatattgagtgaaaatgaatcacttctctgagttctctcacgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctcac