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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctaaatttggacacgtcccttccaaatatgtaggttttctgtgttggtaccatatttttgagtcctaatcttgtttcatcaacctaacagaaattatgatattattctccaagaaatcaataatatgcatgaagaagtcttgaacaattgatatatatttatacagATTGTATGCTCTTTTCTCGTTCGAGACATGGGCATTGACTGGCGTATGGGAGCTGAATGGTTTGAGACTTGCCTCCTCGATTACGACCCTTGTTCCAATT

Basic information

species Vitis vinifera
transcript Vv04s0008g02670.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os06g45100.1 (Oryza sativa), 3'ss of exon 9
gtaaatctaaatttggacacgtcccttccaaatatgtaggttttctgtgttggtaccatatttttgagtcctaatcttgtttcatcaacctaacagaaattatgatattattctccaagaaatcaataatatgca--tgaagaagtcttgaacaattgatatatatttatacagATTGTATGCTCTTTTCTCGTTCGAGACATGGGCATTGACTGGCGTATGGGAGCTGAATGGTTTGAGACTTGCCTCCTCGATTACGACCCTTGTTCCAATT
                                                                      | | |    | | ||||    | |||||||   || || | |  |||||    ||   |    ||  |||   |    |  |    | || |   | | |||||||||| ||||| ||||| || ||||| ||||| ||||| ||||| |||||||||||||||||||| || |||||  | ||||| |||||   ||| ||||
------------------------------------------------------------------gtaaccattggcatcttatcacataagcagaaatgcaga-atgactgcccaagggtacacccaaggccatctgatccaagtatccatctctcat-tgcttctctacagATTGTCTGCTCATTTCTGGTCCGAGATATGGGTATTGATTGGCGAATGGGAGCTGAATGGTTTGAAACATGCCTATTGGATTATGACCCAGCTTCAAATT

upper sequence: Vv04s0008g02670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA04G07870.1 (Glycine max), 3'ss of exon 10
gtaaatctaaatttggacacgtcccttccaaatatgtaggttttctgtgttggtaccatatttttgagtcctaatcttgtttcatcaacctaacagaaattatgatattattctccaagaaatcaataatatgcatgaagaagtcttgaacaattgatatatatttatacagATTGTATGCTCTTTTCTCGTTCGAGACATGGGCATTGACTGGCGTATGGGAGCTGAATGGTTTGAGACTTGCCTCCTCGATTACGACCCTTGTTCCAATT
       | ||   |    | |    |     | | ||   | | |   ||| ||  |  || |  | | | | |||||    | |||   |  ||| | ||  ||  | |  |   |     |||  |  |  || |   |  | |||| | | |||   | |||  ||||||||| || || ||||| ||||| || ||||||||||| ||||| |||||||| |||||||||||||| || ||  | ||||| || || ||||| ||||
------gtgaaccagagagcctattata-gtgtttctacaatatattaattgctagaaatttctacaatacgattcttgg---accaa---agtagataatagtatgctttagtgggattttgcaaacacctttataactgaaacatgaa-actcgattacttttttgacagATTGTGTGTTCATTTCTTGTTCGTGATATGGGCATTGATTGGCGCATGGGAGCAGAATGGTTTGAGACATGTCTTTTGGATTATGATCCATGTTCTAATT
















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|110367735|gb|EC931686.1|EC931686
EST:     ATATGAAGGAACTGTCAGCCACAGGGTTCATGTCAAACCGAGGAAGGCAG                         ATTGTATGCTCTTTTCTCGTTCGAGACATGGGCATTGACTGGCGTATGGGA
genomic: ATATGAAGGAACTGTCAGCCACAGGGTTCATGTCAAACCGAGGAAGGCAGgtaaatctaa ... atttatacagATTGTATGCTCTTTTCTCGTTCGAGACATGGGCATTGACTGGCGTATGGGA
EST: gi|77586218|gb|DV222205.1|DV222205
EST:     ATATGAAGGAACTGTCAGCCACAGGGTTCATGTCAAACCGAGGAAGGCAG                         ATTGTATGCTCTTTTCTCGTTCGAGACATGGG
genomic: ATATGAAGGAACTGTCAGCCACAGGGTTCATGTCAAACCGAGGAAGGCAGgtaaatctaa ... atttatacagATTGTATGCTCTTTTCTCGTTCGAGACATGGG
EST: gi|110389719|gb|EC954579.1|EC954579
EST:     ATATGAAGGAACTGTCAGCCACAGGGTTCATGTCAAACCGAGGAAGGCAG                         ATTGTATGCTCTTTTCTCGTTCGAGACATGGGCATTGACTGGCGTATGGGA
genomic: ATATGAAGGAACTGTCAGCCACAGGGTTCATGTCAAACCGAGGAAGGCAGgtaaatctaa ... atttatacagATTGTATGCTCTTTTCTCGTTCGAGACATGGGCATTGACTGGCGTATGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaatcaataatatgcatgaagaagtcttgaacaattgatatatatttatacagATTGTATGCTCTTTTCTCGTTCGAGACATGGGCATTGACTGGCGTATGGGAGCTGAATGGTTTGAGACTTGCCTCCTCGATTACGACCCTTGTTCCAATT
                                  aattgat  putative branch site (score: 4)
                            ttgaacaattgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatctaaatttggacacgtcccttccaaatatgtaggttttctgtgttggtaccatatttttgagtcctaatcttgtttcatcaacctaacagaaattatgatattattctccaagaaatcaataatatgcatgaagaagtcttgaacaattgatatatatttatacagATTGTATGCTCTTTTCTCGTTCGAGACATGGGCATTGACTGGCGTATGGGAGCTGAATGGTTTGAGACTTGCCTCCTCGATTACGACCCTTGTTCCAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC