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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacactgtttcttgcaagttccagctaattactgcatccattaaagttatgttttcaagggttttgacacaattatttgtggattcttgtgtttaacagGGAATAGAGAAGGGAAGATCTATGTCTGGGAACTGCAGTCCAGCCCCCCTGTTCTCATTGCAAG

Basic information

species Vitis vinifera
transcript Vv19s0014g05210.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G118205_T01 (Zea mays), 3'ss of exon 11
----taacactgtttcttgcaagttccagc-taattactgcatccattaaagttatgttttcaagggttttgacacaattatttgtggattcttgtgtttaacagGGAATAGAGAAGGGAAGATCTATGTCTGGGAACTGCAGTCCAGCCCCCCTGTTCTCATTGCAAG
    ||  ||| | |||||   |||  |   |||  |     ||  | | ||| | |   |   |  |    ||   ||    ||  | | |||      |||||| || |   ||||  ||||||||||||||||| ||||||||||||| || ||  | ||||   |
tatatatgactatatcttg--ggttagattataaggaacaactctctcagagt-acgcggttctgaataacaacc--atctgctgctgctgcttaatgcgaacagGCAACAATAAAGGCGAGATCTATGTCTGGGAAGTGCAGTCCAGCCCGCCCGTCTTAATTGACCG
















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|110378718|gb|EC943862.1|EC943862
EST:     TTGGTTTATCAAATTCTCCTGTGATTTCCATTATAATGCAGCAGCTATAG                         GGAATAGAGAAGGGAAGATCTATGTCTGGGAACTGCAGTCCAGCCCCCCTG
genomic: TTGGTTTATCAAATTCTCCTGTGATTTCCATTATAATGCAGCGGCTATAGgtaatgcaga ... tgtttaacagGGAATAGAGAAGGGAAGATCTATGTCTGGGAACTGCAGTCCAGCCCCCCTG
EST: gi|110374010|gb|EC938475.1|EC938475
EST:     CAAATTCTCCTGTGATTTCCATTATAATGCAGCAGCTATAG                         GGAATAGAGAAGGGAAGATCTATGTCTGGGAACTGCAGTCCAGCCCCCCTG
genomic: CAAATTCTCCTGTGATTTCCATTATAATGCAGCGGCTATAGgtaatgcaga ... tgtttaacagGGAATAGAGAAGGGAAGATCTATGTCTGGGAACTGCAGTCCAGCCCCCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatgttttcaagggttttgacacaattatttgtggattcttgtgtttaacagGGAATAGAGAAGGGAAGATCTATGTCTGGGAACTGCAGTCCAGCCCCCCTGTTCTCATTGCAAG
                 ttttgac  putative branch site (score: 3)
                                       ttcttgt  putative PPT
                        acaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacactgtttcttgcaagttccagctaattactgcatccattaaagttatgttttcaagggttttgacacaattatttgtggattcttgtgtttaacagGGAATAGAGAAGGGAAGATCTATGTCTGGGAACTGCAGTCCAGCCCCCCTGTTCTCATTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - -cttgcaa
- - - - - - - - - - -ccagcta
- - - - - - - - - - - - - - - - - gcatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgga