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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTTACGGGTATTTGACTACTCAAAAGAACAACTAATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAGgtaaataaaaaataaaaacttctaatgctttccctttaaatcaagtaccagatgataccggtttgtcaatatttattttctagaacattttatcacatctcacatacatcattccctagtcatttccctttaatggaccattaaaagctttgaaacaagatcatatttgacatttacatgctgttcccccag

Basic information

species Vitis vinifera
transcript Vv06s0004g03040.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03040.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM5G828139_T01 (Zea mays), 5'ss of exon 5
GTTATTTACGGGTATTTGACTACTCAAAAGAACAACTAATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAGgtaaataaaaaataaaaacttctaatgctttccctttaaatcaagtaccagat--gataccggtttgtcaatatttattttctagaacattttatcacatctcacatacatcattccctagtcatttccc-tttaatggaccattaaaagctttgaaacaagatcatatttgacatttacatgctgttcccccag
|||||||| | |||||||||| | | |||||||||||||||| |||||| |||||||| ||||| || ||  |||||||  | ||||||||| |    ||| | |  || |  | |||     |    ||    |||   |  |  |  |||||  ||  | | |  |  |   |||| |   ||  ||| ||| | || |     |   | | |    ||  |  ||   |  |  || |  |       |  | |  ||| ||||                
GTTATTTAAGAGTATTTGACTTCACGAAAGAACAACTAATATTTGGTGGGAAAAGTTACTATGGTGCACTGTTGTGTTGCTCTTGGAGgtaagttgccaatgacatgttttcctacttagatat--ggtctgccacctatttcgccataggtttcacagaactgaagtatttttacatgtc--caagtctgacagatatgaaaatatgaccgtgtatagttctaccgatgctgtattgcatc-agttgtattattgtccgacttttag---------------

upper sequence: Vv06s0004g03040.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G096070_T01 (Zea mays), 5'ss of exon 8
GTTATTTACGGGTATTTGACTACTCAAAAGAACAACTAATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAGgtaaataaaaaataaaaacttctaatgctttccctttaaatcaagtaccagatgataccggtttgtcaatatttattttctagaacattttatcacatctcacatacatcattccctagtcatttccctttaatggaccattaaaagctttgaaacaagatcatatttgacatttacatgctgttcccccag
|||||||  | ||||| || |  ||||| ||||||||||||| |||||||| |||||||||||| || ||  |||||||  | ||||||||| |   ||       ||| |   | |||   |||     || ||       |||   ||||  |  |  ||||  |||  | | | |   ||||| |   ||                                                                                       
GTTATTTGAGAGTATTCGATTTTTCAAAGGAACAACTAATATTTGGTGGAAGAAGTTATTATGGTGCACTGTTGTGTTGCACTTGGAGgtaagtgtgaat----ggcttgtgtagttttatttttttgggaaatatacccacatatgtgtttccc--ttgttatgctctttatcgtctatccacatattttatg--------------------------------------------------------------------------------------
















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|22011620|gb|BQ796654.1|BQ796654
EST:     ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAG                         CTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
genomic: ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAGgtaaataaaa ... gttcccccagCTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
EST: gi|352786044|gb|FQ481839.1|FQ481839
EST:     ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAG                         CTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
genomic: ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAGgtaaataaaa ... gttcccccagCTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
EST: gi|83275230|gb|DV939326.1|DV939326
EST:     ATATGTGGT-GAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAG                         CTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
genomic: ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAGgtaaataaaa ... gttcccccagCTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
EST: gi|351041729|gb|FQ455939.1|FQ455939
EST:     ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAG                         CTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
genomic: ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAGgtaaataaaa ... gttcccccagCTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
EST: gi|351044962|gb|FQ449216.1|FQ449216
EST:     ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAG                         CTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
genomic: ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAGgtaaataaaa ... gttcccccagCTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
EST: gi|83275347|gb|DV939355.1|DV939355
EST:     GTGTTGTGCCTGGAG                         CTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
genomic: GTGTTGTGCCTGGAGgtaaataaaa ... gttcccccagCTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
EST: gi|351047015|gb|FQ454625.1|FQ454625
EST:     ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAG                         CTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT
genomic: ATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAGgtaaataaaa ... gttcccccagCTTGGATGGAAAATACATTTTGACTGGTGGTGAAGATGATCTAGTTCAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTTACGGGTATTTGACTACTCAAAAGAACAACTAATATGTGGTGGAAAAAGTTATTATGGCGCTCTTCTGTGTTGTGCCTGGAGgtaaataaaaaataaaaacttctaatgctttccctttaaatcaagtaccagatgataccggtttgtcaatatttattttctagaacattttatcacatctcacatacatcattccctagtcatttccctttaatggaccattaaaagctttgaaacaagatcatatttgacatttacatgctgttcccccag

- - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - GGTGGA