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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acggatgtatagaagtgatgtgatacaaaagatttaagttaattctggaataggtatggtaataacttatttttaatttttttggactgatatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGGTGAGCGTGAACAAATGCCTGAACCAATCATTCGAGCTTTTGGCATCCTT

Basic information

species Vitis vinifera
transcript Vv07s0005g00880.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 1
-----acggatgtatagaagtgatgtga-tacaaaagatttaagttaattctggaataggtatggtaataacttatttttaatttttttggactgatatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGGTGAGCGTGAACAAATGCCTGAACCAATCATTCGAGCTTTTGGCATCCTT
        |   |    || | || |   |       ||||    |  || |    |   | |  ||     || | ||   | ||| || |||  | |  |  ||||| ||||| ||||||||||||||||| |||||||| || ||||| |||||    || ||||  ||||| ||||| |||||||| || |||||| || | 
gttcgttcgtcttccttaattaatttccctttctgccatttcctctttttttttttttcatttcttatctgattgtgtt--gtgtttctgaactactgttat--agATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 1
-----acggatgtatagaagtgatgt-gatacaaaagatttaagttaattctggaataggtatggtaataacttatttttaatttttttggactgatatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGGTGAGCGTGAACAAATGCCTGAACCAATCATTCGAGCTTTTGGCATCCTT
        |   |    || | || | | |       ||||    |  || |    |     |  ||     || | ||   | ||| || |||  | |  |  ||||| ||||| ||||||||||||||||| |||||||| || ||||| |||||    || ||||  ||||| ||||| |||||||| || |||||| || | 
gttcgttcgtcttccttaattaatttcgctttctgccatttcctctttttttttttttcacttcttatctgattgtgtt--gtgtttctgaactactgttat--agATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 1
acggatgtatagaagtgatgtgatacaaaagattta--agttaattctggaataggtatggtaataacttatttt-taatttttttggactgatatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGGTGAGCGTGAACAAATGCCTGAACCAATCATTCGAGCTTTTGGCATCCTT
                  | || | |      |||   | |   |||| || ||  | |  || || || ||| | |  | ||| || |||  | |  |  ||||| ||||| ||||||||||||||||| |||||||| || || || |||||    || ||||  ||||| ||||| |||||||| ||||||||| || | 
-----------------gtttgttccttctcctttcccactcttttcttgactatttct--tagtatctgattgtgttgtgtttctgcactactgttat--agATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGACATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCTTTTGGCGTCTTG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 2
acggatgtatagaagtgatgtgatacaaaagatttaagttaattctggaataggtatggtaataacttatttttaatttttttggactgatatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGGTGAGCGTGAACAAATGCCTGAACCAATCATTCGAGCTTTTGGCATCCTT
      ||   | |         |||  ||  |  || ||  |  |    | |    || ||    ||     |  ||| ||||   |  | | | ||||||||||||| || || || || |||||  ||||||| || || || ||||||||||| || | |||||||||||||||  | || ||||||||| || | 
------gttcgggatctgatctttacgcaacgtcgaattttctcttatcctcga---gggaaacgtttcacagtgttttatttg---ttgtgtgtctcagATTGTGGGGAGCCCAGACGCAGAGATCGCTGCAGAACTTCGAAATCGGTGGTGAGCGCGAGCGAATGCCTGAACCAATTGTCCGCGCTTTTGGCGTCTTG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 1
acggatgtatagaagtgatgtgatacaaaagatttaagttaattctggaataggtatggtaataacttattttta-atttttttggactgatatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGGTGAGCGTGAACAAATGCCTGAACCAATCATTCGAGCTTTTGGCATCCTT
                  |  |  |  | |  |||| | ||  | | |    | | | |    ||  |||| | | |||||| |    || | | | ||||||| ||||| ||||| || || |||||  | ||||| || || ||||||||||| || || | |||||| ||||||||| | |||||||||||  || | 
-----------------gttcggaatcagatctttacgatatatatcgttctgatctcgagggaaaatattctcacatttttatttgttgttctgtgtcagATTATGGGGAGCACAGACGCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTG

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|71857320|gb|DT006375.1|DT006375
EST:     TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAA                         ATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTCGATATTGGTGG
genomic: TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAAgttcgttttt ... tatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
EST: gi|352778135|gb|FQ467188.1|FQ467188
EST:     TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAA                         ATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
genomic: TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAAgttcgttttt ... tatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
EST: gi|352782338|gb|FQ470241.1|FQ470241
EST:     TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAA                         ATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
genomic: TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAAgttcgttttt ... tatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
EST: gi|110713618|gb|EE089697.1|EE089697
EST:     TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAA                         ATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTCGATATTGGTGG
genomic: TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAAgttcgttttt ... tatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
EST: gi|352776927|gb|FQ474234.1|FQ474234
EST:     TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAA                         ATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
genomic: TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAAgttcgttttt ... tatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
EST: gi|161712595|gb|FC062197.1|FC062197
EST:     TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAA                         ATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTCGATATTGGTGG
genomic: TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAAgttcgttttt ... tatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
EST: gi|352773939|gb|FQ473071.1|FQ473071
EST:     TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAA                         ATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
genomic: TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAAgttcgttttt ... tatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
EST: gi|33402485|gb|CF208112.1|CF208112
EST:     TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAA                         ATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTCGATATTGGTGG
genomic: TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAAgttcgttttt ... tatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
EST: gi|352773568|gb|FQ472350.1|FQ472350
EST:     TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAA                         ATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
genomic: TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAAgttcgttttt ... tatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG
EST: gi|71858005|gb|DT007060.1|DT007060
EST:     TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAA                         ATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTCGATATTGGTGG
genomic: TTCAGGGAAGAGAAAGATACATTTGGGCCGATTCTTGTTCCTTCTGACAAgttcgttttt ... tatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaataggtatggtaataacttatttttaatttttttggactgatatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGGTGAGCGTGAACAAATGCCTGAACCAATCATTCGAGCTTTTGGCATCCTT
                                             tatctttc  CT-rich tract
              taataacttattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acggatgtatagaagtgatgtgatacaaaagatttaagttaattctggaataggtatggtaataacttatttttaatttttttggactgatatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGGTGAGCGTGAACAAATGCCTGAACCAATCATTCGAGCTTTTGGCATCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - -tgatgtg
- - - - - - - - - - - atacaaa
- - - - - - - - - - - - - - - - - - - - -attctgg