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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTGgtaagttttggttggaaggacttctgctccttccatgctgtgctttttcattcataaattctttttatggtttctgataaaaaaaaaatcgattttattt...

Basic information

species Vitis vinifera
transcript Vv01s0010g01740.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G174286_T03 (Zea mays), 5'ss of exon 11
ATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTGgta--agttttggttggaaggacttctgctccttccatgctgtgctttttcattcataaattctttttatggtttctgataaaaaaaaaatcgattttattt
|||||| |||||||||||||| |||| ||| | ||||||||| || | || ||||| || |||||  | ||||||||||||  | ||||  | |     | | ||   |||  ||   | |    || |||  |    |   ||||    |  |  |         | | | |  || | 
ATGTGCCTTAATGCGTTTGATAAAGCAGCAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattttaatggtgtaaagtactttacctgacacagt-taggattgcatcaaagtttagatttttctataaccaagcgtcttttatttggtagtaat-

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 10
ATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTGgtaagttttggttggaaggacttctg--ctccttccatgctgtgctttttcattcataaattctttttatggtttctgataaaaaaaaaatcgattttattt
|||||||||  ||| || ||| | |  |||||||||||||| || |||||||| || || ||||| ||||||||||||||||  | |   |      | |  |    ||    ||||         || ||  ||  |  ||  ||  | |   |||| | |                  
ATGTGCTTTGCTGCTTTCGATGAGGGGGCAAACCTTGATGTGTTAGATCACCCCATCCTTAACTTCATATATTACCTGgtaacctctctcttagcttaatcatagaatctgatcatgaacattagcttaatatatgtaacctgatttcgttacttgattacag-----------------
















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|30137883|gb|CB923221.1|CB923221
EST:     CAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTG                         TTGGTGGAGATACTGCCTTCATCTCTGGTCCTTTTCATTTTGAGGAAGTTG
genomic: CAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTGgtaagttttg ... acctttacagTTGGTGGAGATACTGCCTTCATCTCTGGTCCTTTTCATTTTGAGGAAGTTG
EST: gi|22013779|gb|BQ798813.1|BQ798813
EST:     CAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTG                         TTGGTGGAGATACTACCTTCATCTCTGGTCCTTTTCATTTTGAGGAAGTTG
genomic: CAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTGgtaagttttg ... acctttacagTTGGTGGAGATACTGCCTTCATCTCTGGTCCTTTTCATTTTGAGGAAGTTG
EST: gi|110411137|gb|EC976839.1|EC976839
EST:     CAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTG                         TTGGTGGAGATACTGCCTTCATCTCTGGTCCTTTTCATTTTGAGGAAGTTG
genomic: CAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTGgtaagttttg ... acctttacagTTGGTGGAGATACTGCCTTCATCTCTGGTCCTTTTCATTTTGAGGAAGTTG
EST: gi|30136439|gb|CB921777.1|CB921777
EST:     CAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTG                         TTGGTGGAGATACTACCTTCATCTCTGGTCCTTTTCATTTTGAGGAAGTTG
genomic: CAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTGgtaagttttg ... acctttacagTTGGTGGAGATACTGCCTTCATCTCTGGTCCTTTTCATTTTGAGGAAGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTGgtaagttttggttggaaggacttctgctccttccatgctgtgctttttcattcataaattctttttatggtttctgataaaaaaaaaatcgattttattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa