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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagataaagacgcttaatattaatgcccttttgtacattcatcatcatcatcatccccatcctcattgatgaactctgttcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG

Basic information

species Vitis vinifera
transcript Vv09s0002g01800.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 17
gtaagataaagacgcttaatattaa-tgcccttttgtacattcatcatcatcatcatcccc--atcctcattgatgaactctgttcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG
|| |||  |    | | | | ||   |    ||| ||  ||| ||     |||   | | |  ||| || |  ||   ||   | | |  ||||| || | |||||| || || ||  | ||  |||| |||||||||||||| ||||||||||| ||||| || ||||||||||||||||| || ||||
gtgagaacagtttggtcatttttcccttttatttcgtttattaattgcagtcacttttctcttatcttcgtgcattg-ctgactacatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCGGGTGCTGAAGAATTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 17
gtaagataaagacgcttaatattaatgcccttttgtacattcatcatcatcatcatcccc--atcctcattgatgaactctgttcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG
|| |||  |    | | | | ||       |||  | |||| ||     | |   | | |  ||| |  |  ||   ||   | | |  ||||| || | |||||| || || ||  ||||  |||| || ||||||||||| ||||||||||| ||||| || ||||||||||||||||| || ||||
gtgagaacagtttggtcattttttcctttatttctttcattaattgcagttacttttctcttatctttgtgcattg-ctgactacatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG
















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|22008294|gb|BQ793328.1|BQ793328
EST:     CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTTGCCATTGGGTCTG                         CCGAGAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
genomic: CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTGgtaagataaa ... tcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
EST: gi|110407843|gb|EC973460.1|EC973460
EST:     TTGTGCCATCATCAATCCTCCTCAGTCAGGCATTTTAGCCATTGGGTCTG                         CCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
genomic: CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTGgtaagataaa ... tcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
EST: gi|22009486|gb|BQ794520.1|BQ794520
EST:     CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTTGCCATTGGGTCTG                         CCGAGAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
genomic: CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTGgtaagataaa ... tcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
EST: gi|33405959|gb|CF211586.1|CF211586
EST:     CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTG                         CCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTNAAGTTTGCCT
genomic: CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTGgtaagataaa ... tcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
EST: gi|34363482|gb|CF405067.1|CF405067
EST:     CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTTGCCATTGGGTCTG                         CTGAGAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
genomic: CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTGgtaagataaa ... tcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
EST: gi|161714484|gb|FC064459.1|FC064459
EST:     CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTTGCCATTGGGTCTG                         CTGAGAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
genomic: CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTGgtaagataaa ... tcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
EST: gi|32250355|gb|CD716174.1|CD716174
EST:     CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTTGCCATTGGGTCTG                         CCGAGAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
genomic: CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTGgtaagataaa ... tcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
EST: gi|22009599|gb|BQ794633.1|BQ794633
EST:     CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTTGCCATTGGGTCTG                         CCGAGAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
genomic: CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTGgtaagataaa ... tcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
EST: gi|30132039|gb|CB917378.1|CB917378
EST:     CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTTGCCATTGGGTCTG                         CCGAGAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT
genomic: CTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTGgtaagataaa ... tcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattcatcatcatcatcatccccatcctcattgatgaactctgttcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG
                             cattgat  putative branch site (score: 4)
                                       ctctgttcttttgc  putative PPT
                                            ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagataaagacgcttaatattaatgcccttttgtacattcatcatcatcatcatccccatcctcattgatgaactctgttcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG