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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcttcattcccctcgaggcttcatcagtcttcgtccttttaatctgtattttctcgttctctgatttttcttcttcttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG

Basic information

species Vitis vinifera
transcript Vv03s0063g00140.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G11530.2 (Glycine max), 3'ss of exon 1
------------------------------------------------------gtaagctcttcattcccctcgaggcttcatcagtcttcgtccttttaatctgtattttctcgt----tctctgatttt-tcttcttcttgt-tgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG
                                                       |  | | || |||    |  |      |    | ||         ||||| | ||||   |     | | ||||    |  |  | |||| |  ||||||| || || |||||||| ||||||||||| || ||||||||||| || || ||||||||||| ||  | || |||||
gtaccaccccaattacattcctttgttaaaaaagaaaaaaaaaatctttttttcttttggtttttattttattttatataatagttatgttgaaaacaaaaatctttttttttcgggggggtgtttgataaaatggttatgttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG

upper sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 1
-----------------------------------------gtaagctcttcattcccctcgaggcttcatcagtcttcgtccttttaa-------tctgtattttctcgttctctgattt--ttcttcttcttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG
                                           ||  ||||  |  |  | | |  ||    |   |   |   || ||       ||| | ||||   | | | ||||    |  || | ||   |  ||||||| || || || ||||| ||||||||||| || ||||||||||| || || ||||||||||| ||  | || |||||
gtaccaccccaattgcattcctttgataaaaagaaaaagaaaaaaaatctttttctcttttgggtttttgataaaatggttatgttgaaaaaaaaatctattttttgggggtttttgataaaatggttatgctgtgtttagTATATTCTGGAGACAAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG
















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|161707477|gb|FC055995.1|FC055995
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|352795208|gb|FQ477318.1|FQ477318
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCTGAATCCATGAAGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|33409666|gb|CF215293.1|CF215293
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|110392855|gb|EC957377.1|EC957377
EST:     TGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
genomic: TGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|110392663|gb|EC956866.1|EC956866
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCTGAATCCATGAAGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|77586769|gb|DV222527.1|DV222527
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCTGAATCCATGAGGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|33407984|gb|CF213611.1|CF213611
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTACCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCTGAATCCATGAAGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|34548696|gb|CF516928.1|CF516928
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCTGAATCCATGAAGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|37185411|gb|CF604764.1|CF604764
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCTGAATCCATGAAGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|110378003|gb|EC943111.1|EC943111
EST:     GAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCTGAATCCATGAAGGAG
genomic: GAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|34550193|gb|CF518411.1|CF518411
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCTGAATCCATGAAGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|110372307|gb|EC936462.1|EC936462
EST:     CTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCTGAATCCATGAAGGAG
genomic: CTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|110378272|gb|EC943395.1|EC943395
EST:     GCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
genomic: GCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|110365089|gb|EC928834.1|EC928834
EST:     GATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
genomic: GATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|352794669|gb|FQ475167.1|FQ475167
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCTGAATCCATGAAGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
EST: gi|33409385|gb|CF215012.1|CF215012
EST:     ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAG                         TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG
genomic: ACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctctt ... cttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtccttttaatctgtattttctcgttctctgatttttcttcttcttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG
            tctgtattttctcgtt  CT-rich tract
      ttttaatctgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctcttcattcccctcgaggcttcatcagtcttcgtccttttaatctgtattttctcgttctctgatttttcttcttcttgttgcagTATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA