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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattggatttttatttcaggttcctatggtgaatcaatgtgcttgaaataatttcttgttctttctagcattatttacaaaatgtggttagaattgcattctttccaggtcccttagctttcaaatatgtcactcctgttcttatttggtgccaagttaggaagtaataataagtcccactttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGGATGTACTCACGACTAT

Basic information

species Vitis vinifera
transcript Vv11s0016g02870.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02870.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g53700.1 (Oryza sativa), 3'ss of exon 6
gtattggatttttatttcaggttcctatggtgaatcaatgtgcttgaaataatttcttgttctttctagcattatttacaaaatgtggttaga-attgcattctttccaggtcccttagctttcaaatatgtcactcctgttcttatttggtgccaagttaggaagtaataataagtcccactttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGGATGTACTCACGACTAT
                                      | |  |||  | ||  ||   ||      | ||||||| | | |      | |   || | || | ||  | ||   ||| || || | ||     | | | |   |      |  |    || | | ||   ||          || |||||||||| |||||||||||||| ||||||||||||||||||||||| || || ||| | || ||| | |
-------------------------------------gtattgttggca-aacatcaaattta----accattattcagagacaaaactcaactatggtataccttttatgtagttta-ctgtctagtagactgc-cttatatgttcaccatttctttatacgcaatatggatggtcttgttattttgcagATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGT

upper sequence: Vv11s0016g02870.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G005036_T01 (Zea mays), 3'ss of exon 6
gtattggatttttatttcaggttcctatggtgaatcaatgtgcttgaaataatttcttgttctttctagcattatttacaaaatgtggttagaattgcattctttccaggtcccttagctttcaaatatgtcactcc-tgttcttatttggtgccaagttag-gaagtaataataagtcccactttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGGATGTACTCACGACTAT
                                                                                             ||| | ||||  |   ||     | |  ||| || ||    | | | | || || |  |      | |  |   |  | || | |     | |||| ||||||| ||||||||||| || || |||||||||||||| |||||||| || ||| | || ||| | |
------------------------------------------------------------------------------------------gccatttc-ttctagcggtgttaaaaaacaatcacatgtgctgttgcatatgctaatctaatagtgcttcaaaggtatgttgatcaattt-gttgtctgtagATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT

upper sequence: Vv11s0016g02870.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G36040.1 (Glycine max), 3'ss of exon 6
gtattggatttttatttcaggttcctatggtgaatcaatgtgcttgaaataatttcttgttctttctagcattatttacaaaatgtggttagaattgcattctttccaggtcccttagctttcaaatatgtc-actcctgttcttatttggtgccaagttaggaagtaataataagtcccactttc--tgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGGATGTACTCACGACTAT
|| |||   |  | | | |  ||    || |   |   ||  ||||||||    | || ||||||  ||  |   ||| || || |   |  ||| | ||   |    |||  ||||      || |||||  |||| |     |||        ||||| | |  | |   ||  | |   ||||  |  |||||||| ||||||| |||||||| ||||| |||||||| ||||| ||||||||||| ||||| ||||
gttttga--taatgtcttatattttcttgct---tttctgcacttgaaatttccttttcttcttttaag-gtggcttaaaatatatcagtgtaat-gtatgtctagttggtttctta------aagtatgtttactctttacaatatgattcattaagtttgtattttactgtattttctcatttcactatagATGCTATTGGGAGGCGGTGGATCATTCTCAGCTGGTGGACCTGGTAAAGGGATGTATTCACGGCTAT

upper sequence: Vv11s0016g02870.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G03580.1 (Glycine max), 3'ss of exon 5
gtattggatttttatttcaggttcctatggtgaatcaatgtgcttgaaataatttcttgttctttctagcattatttacaaaatgt---ggttagaattgcattctttccaggtcccttagctttcaaatatgtc-actcctgttcttatttggtgccaagttaggaagtaataataagtcc-cacttt-ctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGGATGTACTCACGACTAT
|| |||   |  | | | |  ||    || |   |   ||  |||||||| |  | |  ||||||  ||  |   ||| || || |    ||  | | || ||   |    |||  ||||      || |||||  || | |     |||        ||||| | |  |||   ||  ||| || ||| ||  |||||||| ||||||| |||||||| ||||| |||||||| ||||| ||||||||||| ||||| ||||
gttttga--taatgtcttacattttcttgct---tttctgcacttgaaatcacctttccttcttttaag-gtggcttaaaatatatcagagtatggactgtatgtctagttggtttctta------aagtatgtttacactttacaatatgattcattaagtttgtatttaactgtatttcctcattttactatagATGCTATTGGGAGGTGGTGGATCATTCTCAGCTGGTGGACCTGGTAAAGGGATGTATTCACGGCTAT

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|32247970|gb|CD713789.1|CD713789
EST:     CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAG                         ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
genomic: CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatt ... ctttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
EST: gi|110716318|gb|EE091196.1|EE091196
EST:     CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAG                         ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
genomic: CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatt ... ctttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
EST: gi|110382252|gb|EC938898.1|EC938898
EST:     CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAG                         ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
genomic: CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatt ... ctttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
EST: gi|22014250|gb|BQ799284.1|BQ799284
EST:     CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAG                         ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
genomic: CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatt ... ctttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
EST: gi|32268962|gb|CD718121.1|CD718121
EST:     CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAG                         ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG
genomic: CCGGTGGTTGGCATAAGGAGAAGGAAGCAATGACTTTGACAGTTCTTCAGgtattggatt ... ctttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttcttatttggtgccaagttaggaagtaataataagtcccactttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGGATGTACTCACGACTAT
                                        tcccactttct  CT-rich tract
                           aagtaataataagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattggatttttatttcaggttcctatggtgaatcaatgtgcttgaaataatttcttgttctttctagcattatttacaaaatgtggttagaattgcattctttccaggtcccttagctttcaaatatgtcactcctgttcttatttggtgccaagttaggaagtaataataagtcccactttctgcagATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGGATGTACTCACGACTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG