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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattatttctagtgcatgatattacctagatgtctcaatgttttgttttcttattctagatattagtttattaagttattattttttacactgattgtggagggttacgtaatcatatctgatttctcatattcacttctcttaagctcctcaacctcctccctatctcttctaaatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGATGTTTATAGCTTTGGGGTTGTGCTTTTGGAAGCAATTACTGGAAGAGAT

Basic information

species Vitis vinifera
transcript Vv14s0060g00460.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G22550.1 (Glycine max), 3'ss of exon 4
gtaagtattatttctagtgcatgatattacctagatgtctcaatgttttgttttcttattctagatattagtttattaagttattattttttacactgattgtggagggttacgtaatcatatctgatttctcatattcacttctcttaagctcctcaacctcctccctatctcttctaaatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGATGTTTATAGCTTTGGGGTTGTGCTTTTGGAAGCAATTACTGGAAGAGAT
                                              | ||| || || | ||      ||      || ||  ||  ||| | | || | ||  |  | ||   | |     |   ||  || ||||| | |  | |   |  |  ||                   ||||  | |||||||||||||||||||||||||||||||||| ||| | ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||||
---------------------------------------------gtctgtatttttgtgctcttccctatggagctatgtcctt--tttctgccctcaatggaggagctttgatga----gttcaatccct-atatttattcttttctcgtgctcca-------------------taaaattgacagATATGTGGCTCCTGAATATGCAAATACTGGTCTTCTAAATGAAAAAAGTGATGTTTATAGCTTTGGTGTTGTGCTATTGGAAGCAATTACTGGAAGAGAT

upper sequence: Vv14s0060g00460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G28490.1 (Glycine max), 3'ss of exon 4
gtaagtattatttctagtgcatgatattacctagatgtctcaatgttttgttttcttattctagatattagtttattaagttattattttttacactg-attgtggagggttacgtaatcatatctgatttctcatattcacttctcttaagctcctcaacctcctccctatctcttctaaatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGATGTTTATAGCTTTGGGGTTGTGCTTTTGGAAGCAATTACTGGAAGAGAT
                                              |  || || || | ||      ||      || | | || || |  || |   |||||  || |  || |       |  |||  || | ||| | |                 | | ||  ||  |||    |||| | |||||||||||||||||||||||||||||||||| ||| | ||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||||||||
---------------------------------------------gtccgtatttttgtgctcttccctatagagctatgctctttttctgcactcaatattgttaagaggaactttgatgagttggatc-cttacatttatt-----------------ctttctttcttgctccataaaat-tgacagATATGTGGCTCCTGAATATGCAAATACTGGTCTTCTAAATGAAAAAAGTGATGTTTATAGCTTTGGTGTTGTGCTATTGGAAGCAATAACTGGAAGAGAT

upper sequence: Vv14s0060g00460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G38800.1 (Glycine max), 3'ss of exon 4
gtaagtattatttctagtgcatgatattacctagatgtctcaatgttttgttttcttattctagatattagtttattaagttattattttttacactgattgtggagggttacgtaatcatatctgatttctcatattcacttctcttaagctcctcaacctcctccctatctcttctaaatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGATGTTTATAGCTTTGGGGTTGTGCTTTTGGAAGCAATTACTGGAAGAGAT
                                                                               || | || ||||    ||   ||  || | || |  |  |  |    |||  | | |||   |      ||  |  ||    |      | |    |  | || | |||||||||||||||||||||||||||||||||||||| | ||||| || |||||||||||||||||||| ||| |||| ||||||| ||||||||| ||||||
-------------------------------------------------------------------------------gtcagtaatttt-gtgct--ctgctgaagttttcccatgctcagt--attgttaaaattttgtaagaaaaaattattcttattttcttttttgctataaatatttcacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTCTAAATGAGAAGAGTGATGTTTATAGCTTTGGTGTTTTGCTATTGGAAGGAATTACTGGTAGAGAT

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|110725970|gb|EE102993.1|EE102993
EST:     TTGGGTGCTGGGAAAAGTCATATCACAACTCGAGTTATGGGAACCTTTGG                         ATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGA
genomic: TTGGGTGCTGGGAAAAGTCATATCACAACTCGAGTTATGGGAACCTTTGGgtaagtatta ... aatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGA
EST: gi|110415976|gb|EC981921.1|EC981921
EST:     TTGGGTGCTGGGAAAAGTCATATCACAACTCGAGTTATGGGAACCTTTGG                         ATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGA
genomic: TTGGGTGCTGGGAAAAGTCATATCACAACTCGAGTTATGGGAACCTTTGGgtaagtatta ... aatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGA
EST: gi|34543460|gb|CF511692.1|CF511692
EST:     TTGGGTGCTGGGAAAAGTCATATCACAACTCGAGTTATGGGAACCTTTGG                         ATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGA
genomic: TTGGGTGCTGGGAAAAGTCATATCACAACTCGAGTTATGGGAACCTTTGGgtaagtatta ... aatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGA
EST: gi|110403999|gb|EC969916.1|EC969916
EST:     TTGGGTGCTGGGAAAAGTCATATCACAACTCGAGTTATGGGAACCTTTGG                         ATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGA
genomic: TTGGGTGCTGGGAAAAGTCATATCACAACTCGAGTTATGGGAACCTTTGGgtaagtatta ... aatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGA
EST: gi|161719711|gb|FC065745.1|FC065745
EST:     TTGGGTGCTGGGAAAAGTCATATCACAACTCGAGTTATGGGAACCTT-GG                         ATATGTGGCTCCTGA-TATGCAA-TACTGGCCTTT
genomic: TTGGGTGCTGGGAAAAGTCATATCACAACTCGAGTTATGGGAACCTTTGGgtaagtatta ... aatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcacttctcttaagctcctcaacctcctccctatctcttctaaatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGATGTTTATAGCTTTGGGGTTGTGCTTTTGGAAGCAATTACTGGAAGAGAT
                                        ttctaaa  putative branch site (score: 2)
                         cctcctccctatctct  CT-rich tract
                                           taaatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattatttctagtgcatgatattacctagatgtctcaatgttttgttttcttattctagatattagtttattaagttattattttttacactgattgtggagggttacgtaatcatatctgatttctcatattcacttctcttaagctcctcaacctcctccctatctcttctaaatgttacagATATGTGGCTCCTGAATATGCAAATACTGGCCTTTTGAATGAAAAAAGTGATGTTTATAGCTTTGGGGTTGTGCTTTTGGAAGCAATTACTGGAAGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA