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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcaactcgttgctgatgatttttcttctacttttttttttggggggttaaaaaacattaactggtactacctttttttcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT

Basic information

species Vitis vinifera
transcript Vv11s0052g01710.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 16
gtatgtcaactcgttgctgatgatttttcttctactt---ttttttttggggggttaaaaaacattaactggtactacctttttttcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
||  ||  | |   |  |        ||  | || |    |  || |      | ||  |  ||| |  || || |   ||  | |  |||  |||| ||||| || ||||| |||||||||||||||||||||||
gtgagttgaattaataatatgttgccttgatatattcaggtaattatcaatatgatactattcatgagttg-taatgttttgatatggttg-tagGGTGGGCTTGCACCTGGTGGATTCAACTTTGATGCCAAATT
















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|351031975|gb|FQ460232.1|FQ460232
EST:     TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAAT                         GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
genomic: TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAATgtatgtcaac ... tcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
EST: gi|351032492|gb|FQ458857.1|FQ458857
EST:     TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAAT                         GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
genomic: TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAATgtatgtcaac ... tcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
EST: gi|349809734|gb|FQ398359.1|FQ398359
EST:     TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAAT                         GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
genomic: TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAATgtatgtcaac ... tcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
EST: gi|349811710|gb|FQ409707.1|FQ409707
EST:     TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAAT                         GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
genomic: TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAATgtatgtcaac ... tcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
EST: gi|349812955|gb|FQ411195.1|FQ411195
EST:     TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAAT                         GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
genomic: TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAATgtatgtcaac ... tcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
EST: gi|351032512|gb|FQ458877.1|FQ458877
EST:     TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAAT                         GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
genomic: TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAATgtatgtcaac ... tcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
EST: gi|22015436|gb|BQ800470.1|BQ800470
EST:     TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAAT                         GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
genomic: TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAATgtatgtcaac ... tcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
EST: gi|352786892|gb|FQ481267.1|FQ481267
EST:     TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTTGTCCGAAAT                         GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
genomic: TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAATgtatgtcaac ... tcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
EST: gi|349820047|gb|FQ404769.1|FQ404769
EST:     TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAAT                         GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
genomic: TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAATgtatgtcaac ... tcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
EST: gi|29784962|gb|CB341547.2|CB341547
EST:     TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAAT                         GGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
genomic: TTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAATgtatgtcaac ... tcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttggggggttaaaaaacattaactggtactacctttttttcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT
                      cattaac  putative branch site (score: 2)
                                  ctacctttttttcatt  putative PPT
              ttaaaaaacattaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcaactcgttgctgatgatttttcttctacttttttttttggggggttaaaaaacattaactggtactacctttttttcattgacagGGAGGGCTGGCCCCTGGAGGATTCAACTTTGATGCCAAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT