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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATTGTTGCTGATAACTACTTCACTGGATCTAAAGATAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattctcatttgctttgtcattacaaggtggacacaatcaggactgttaaacgcctttccttgtcaagttctttatttgctggatgggttcatgtc...

Basic information

species Vitis vinifera
transcript Vv13s0019g00840.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 4
GTGATTGTTGCTGATAACTACTTCACTGGATCTAAAGATAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattctcatttgctttgtcattacaaggtggac-acaatca-ggactgttaaacgcctttccttgtcaagttctttatttgctggatgggttcatgtc-
|| ||||| || || ||||  |||||||| || ||||| ||||||| ||| ||||| || || |||||||||||||| || ||||||||||||  |  ||||  |  ||   |||     || || |   | |   |||  |||     |||   ||  |     ||| || | |  |    ||   |   
GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgcta-cattctcagtgcatttagttcatgaactattgttacatactagtaataaagttttactgctagcaagttttttcgttcaa--aatttgagaaa

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
GTGATTGTTGCTGATAACTACTTCACTGGATCTAAAGATAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattctcatttgctttgtcattacaaggtggacacaatcaggactgttaaacgcctttccttgtcaagttctttatttgctggatgggttcatgtc-
|| ||||||||||||||||  |||||||| || ||||| ||||||| ||| |||||||| || |||||||||||||| || ||||||||||     ||  || ||| ||    |  ||| |      | ||    || | | | |    |    || | |  |  |   |  |  |||  |  ||    
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctggatagtcaatga-taaataaac

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
GTGATTGTTGCTGATAACTACTTCACTGGATCTAAAGATAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattctcatttgctttgtcattacaaggtggacacaatcaggactgttaaacgcctttccttgtcaagttctttatttgctggatgggttcatgtc
|| ||||||||||||||||  |||||||| || ||||||||||||| ||| ||||| || || |||||||||||||| || || |||||||     ||  || |   ||       |||        | ||    || | | | |    |    || | |     |   |     |  | |  ||   
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagttagacatgcatgcttaagacattttaagtcctccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa

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|110700937|gb|EE078028.1|EE078028
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|71860037|gb|DT009092.1|DT009092
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|71882833|gb|DT031888.1|DT031888
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110703601|gb|EE080591.1|EE080591
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110702160|gb|EE080556.1|EE080556
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|156736486|gb|EV240607.1|EV240607
EST:     GAGG-AATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: GAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|71863746|gb|DT012801.1|DT012801
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|71859225|gb|DT008280.1|DT008280
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110357315|gb|EC920771.1|EC920771
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110723901|gb|EE099257.1|EE099257
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110720753|gb|EE096961.1|EE096961
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110721290|gb|EE098120.1|EE098120
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110727671|gb|EE104694.1|EE104694
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110714087|gb|EE090592.1|EE090592
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110719051|gb|EE096588.1|EE096588
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGATGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110687991|gb|EE066031.1|EE066031
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|33407947|gb|CF213574.1|CF213574
EST:     TAACCTGAGAAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|71862913|gb|DT011968.1|DT011968
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110692310|gb|EE071412.1|EE071412
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|110356627|gb|EC919593.1|EC919593
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|30299440|gb|CB976234.1|CB976234
EST:     TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
EST: gi|71860871|gb|DT009926.1|DT009926
EST:     TAACCTGAGGAAATGGATTGGTCATCCAGGATTTGAGCTTATTCGTCATG                         ATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT
genomic: TAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattct ... attcatccagATGTTACTGAGCCATTGTTGATTGAGGTTGATCAAATATACCATCTTGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATTGTTGCTGATAACTACTTCACTGGATCTAAAGATAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattctcatttgctttgtcattacaaggtggacacaatcaggactgttaaacgcctttccttgtcaagttctttatttgctggatgggttcatgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttcc