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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactgattttgtttgagattaccaagttccatcttgtaattgctttttggatgaattaatgccggaaaggttgctgttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGAGTCTTGTGTCGTATGGCTGAAGAAGCTGACCTTTTTGGGGACACTGTTC

Basic information

species Vitis vinifera
transcript Vv11s0016g03070.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G01070.1 (Glycine max), 3'ss of exon 6
gtgactgattttgtttgagattaccaagttccatcttgtaattgctt-tttggatgaattaatgccggaaaggttgctgttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGAGTCTTGTGTCGTATGGCTGAAGAAGCTGACCTTTTTGGGGACACTGTTC
        |  ||  |     || ||| |     |||  |||  ||  | || ||  || ||| |     |  |   ||||    ||||||||||||||||| |||||||||||||||||||| ||||||||| | ||||| ||||     |||||||||||||||||| | ||||| || |||||||
-------gtaatggctat--ctatcaattattggctta-aatgactaatgtgcatttat-aatactcttcaactc-ttgtt--tgcagATTTTTGAGAAGATAATTTCTGGTATGTATTTGGGTGACATTGTAAGGAGAGTTTTGTTGAAGATGGCTGAAGAAGCTGACTTCTTTGGAGATACTGTTC

upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G01060.3 (Glycine max), 3'ss of exon 6
gtgactgattttgtttgagattaccaagtt-ccatct-tgtaattgctttttggatgaat-taatgccggaaaggttgctgttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGAGTCTTGTGTCGTATGGCTGAAGAAGCTGACCTTTTTGGGGACACTGTTC
              |   ||||| | |  |  |||   | ||| ||  |  ||      | |||| |     |  ||  ||||    ||||||||||||||||| |||||||||||||||||||| || |||||| | ||||| ||||      |||||||||||| |||| | ||||| || |||||||
-------------gtaatgattatctatctatcattggtttaaatgactaatgtgcacttataatactcttcaa-ttcttgtt--tgcagATTTTTGAGAAGATAATTTCTGGTATGTATTTGGGTGAAATTGTAAGGAGAGTTTTGTTGAAGTTGGCTGAAGAAGTTGACTTCTTTGGAGATACTGTTC

upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G12190.1 (Glycine max), 3'ss of exon 6
gtgactgattttgtttgagattaccaagtt-ccatct-tgtaattgctttttggatgaat-taatgccggaaaggttgctgttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGAGTCTTGTGTCGTATGGCTGAAGAAGCTGACCTTTTTGGGGACACTGTTC
              |    |||| | |  |  |||   | ||| ||  |  ||      | ||||||     |  |     |||   |||||||||||||||||  |||||||||||||||| || ||||||||| | ||||| ||||     ||||| ||||||| |||| | ||||| || |||||||
-------------gtaataattatctatctatcattggtttaaatgactaatgtgcatgtataatgctcttcaactcttctttg---cagATTTTTGAGAAGATAGTTTCTGGTATGTATTTAGGTGACATTGTAAGGAGAGTTTTGTTGAAGATGGCGGAAGAAGTTGACTTCTTTGGAGATACTGTTC

upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G35890.1 (Glycine max), 3'ss of exon 6
gtgactgattttgtttgagattaccaagttccatcttgtaattgctttttggatgaat-taatgccggaaaggtt--gctgttgt-cacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGAGTCTTGTGTCGTATGGCTGAAGAAGCTGACCTTTTTGGGGACACTGTTC
                |  || | ||  | | || || || ||| ||  | |||  || | |  |    ||  ||   || |  | ||||||||||||||||  | |||||||| ||||||||||| || |||||| | ||||  || | |   ||||| |||||||||||  ||||||| || |||||||
----------------gtaataatcatctactatatt-tatttgtttagtcgatctatgttactctaacaatattccactatgattcacagATTTTTGAGAAATTGATTTCTGGCATGTATTTGGGGGAAATTGTAAGGAGAGCTTTATTTAAGATGGCCGAAGAAGCTGATTTTTTTGGAGATACTGTTC

upper sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G03730.1 (Glycine max), 3'ss of exon 6
gtgactgattttgtttgagattaccaagttccatcttgtaattgctttttggatgaat-taatgccggaaaggtt--gctgttgt-cacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGAGTCTTGTGTCGTATGGCTGAAGAAGCTGACCTTTTTGGGGACACTGTTC
                |  || | ||  | | || || || ||| ||  | ||   || |||  |    ||  ||   || |  | ||||||||||||||||  | |||||||| ||||||||||| ||  ||||| | ||||  || |     ||||| |||||||||||| ||||||| || |||||||
----------------gtaataatcatctactatatt-tatttgtttaatcgacctatctaactctaacaatattccactatgattcacagATTTTTGAGAAATTGATTTCTGGCATGTATTTGGGGGAAGTTGTAAGGAGAGCTTTATTGAAGATGGCCGAAGAAGCTGACTTTTTTGGCGATACTGTTC

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|161713800|gb|FC063788.1|FC063788
EST:     CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAG                         ATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
genomic: CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAGgtgactgatt ... gttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
EST: gi|110687027|gb|EE064076.1|EE064076
EST:     CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAG                         ATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
genomic: CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAGgtgactgatt ... gttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
EST: gi|110713107|gb|EE088738.1|EE088738
EST:     CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAG                         ATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
genomic: CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAGgtgactgatt ... gttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
EST: gi|294965564|gb|GW837163.1|GW837163
EST:     CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAG                         ATTTTTGAGGAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
genomic: CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAGgtgactgatt ... gttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
EST: gi|110410290|gb|EC975970.1|EC975970
EST:     CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAG                         ATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
genomic: CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAGgtgactgatt ... gttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
EST: gi|110377656|gb|EC942735.1|EC942735
EST:     CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAG                         ATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
genomic: CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAGgtgactgatt ... gttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
EST: gi|110723174|gb|EE100188.1|EE100188
EST:     CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAG                         ATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA
genomic: CAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAGgtgactgatt ... gttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgtaattgctttttggatgaattaatgccggaaaggttgctgttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGAGTCTTGTGTCGTATGGCTGAAGAAGCTGACCTTTTTGGGGACACTGTTC
                       aattaat  putative branch site (score: 3)
                    atgaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgactgattttgtttgagattaccaagttccatcttgtaattgctttttggatgaattaatgccggaaaggttgctgttgtcacagATTTTTGAGAAGATTATTTCTGGTATGTATTTGGGAGACATTGTACGCAGAGTCTTGTGTCGTATGGCTGAAGAAGCTGACCTTTTTGGGGACACTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA