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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttgtgtctacttcttgtatcttgttcaatagtttttgaccctgcaatagatgagcatcaactgggatgcctaacctttattcattcctttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGGCATAAAGCAAATCATCCCTGATCAAGAGCTTTCCTTATTTTCCCTCTTG

Basic information

species Vitis vinifera
transcript Vv13s0019g04120.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G07160.2 (Glycine max), 3'ss of exon 4
atgttgtgtctacttcttgtatcttgttcaata----gtttttgac-cctgcaatagatgagcatcaactgggatgcctaacctttattcattcctttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGGCATAAAGCAAATCATCCCTGATCAAGAGCTTTCCTTATTTTCCCTCTTG
 | |   | |||  | ||  ||||      | |    |||||  |   |  |  |  |  |  ||    |  ||| | |||   |  |        || |   ||||| ||||| |||||||| || || |||||  | || |||||| | |||||||| |||||||| || || |||||||||||| | ||  ||    |    
-tttctaggctatctgttaaatctgaagagacattcagttttctatatccaccttgaacaaatattctttttgat-cttaatactcttgtggaatgttct---agTTACATGCCACTTTCTGGATTTCATGGAGTTGTATCTGGTTTCTTGGTTGGCATTAAGCAAATTATACCAGATCAAGAGCTTCCTTTCATTAAGATAAAA
















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|71857591|gb|DT006646.1|DT006646
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|71861495|gb|DT010550.1|DT010550
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|71860611|gb|DT009666.1|DT009666
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|30255678|gb|CB971810.1|CB971810
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|110689183|gb|EE065183.1|EE065183
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|351025044|gb|FQ433461.1|FQ433461
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|71862645|gb|DT011700.1|DT011700
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|110418019|gb|EC984128.1|EC984128
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|110381307|gb|EC946633.1|EC946633
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|351037220|gb|FQ457053.1|FQ457053
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|71863408|gb|DT012463.1|DT012463
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|22010776|gb|BQ795810.1|BQ795810
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|22010775|gb|BQ795809.1|BQ795809
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|30255752|gb|CB971884.1|CB971884
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|349828743|gb|FQ418478.1|FQ418478
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|110721127|gb|EE097773.1|EE097773
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|71860253|gb|DT009308.1|DT009308
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|351017619|gb|FQ435972.1|FQ435972
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|161714461|gb|FC064448.1|FC064448
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
EST: gi|110402278|gb|EC959746.1|EC959746
EST:     TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCT                         TTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG
genomic: TTCATCACAGCTATCGCCTTGTACTATATAACAAGGCAGGAAAATTACCTgtaagtattc ... tttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatagatgagcatcaactgggatgcctaacctttattcattcctttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGGCATAAAGCAAATCATCCCTGATCAAGAGCTTTCCTTATTTTCCCTCTTG
                         gcctaac  putative branch site (score: 2)
                               cctttattcattcctt  CT-rich tract
                                 tttattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttgtgtctacttcttgtatcttgttcaatagtttttgaccctgcaatagatgagcatcaactgggatgcctaacctttattcattcctttttggtagTTATATGCCTCTTTCTGGCTTCCACGGAGTCCTTTCAGGTTTCCTAGTTGGCATAAAGCAAATCATCCCTGATCAAGAGCTTTCCTTATTTTCCCTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
-tgttgtg
- - - - -ctacttc
- - - - - - - - - - - - - - - - - - - - -ccctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatgcc