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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctgatttagtttgcaatatttttcagaaaggtttttactcattcttgatactgctttcctcaattttggattcaagaaactaatatttaaatgagggtgtattagaaattcctgtcaaattcaccttgctggttctttttgtgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGATTTTGCTCTTGAACTACATTGGAGGGGCTACCAATCCTGGAATTTTGTC

Basic information

species Vitis vinifera
transcript Vv07s0005g02540.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G27890.1 (Glycine max), 3'ss of exon 7
gtaaat-ctgatttagtttgcaatatttttcagaaaggtttttactcattcttgatactgctttcctcaattttgg-attcaagaaactaatatttaaatgagggtgtattagaaattcctgtcaaattcaccttgctggttctttttgt--gttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGATTTTGCTCTTGAACTACATTGGAGGGGCTACCAATCCTGGAATTTTGTC
|| | |  ||||||| |    || | ||    | | | |||  || || |         |  ||  | | | ||   ||||| |  |  | |    |     | |||  ||  |      || |   ||         |    | |||||  |||  |||||||| ||||||||||||||||| || || ||||||||||| ||||||||| || | |||||||| ||||||||||| || || ||| |||||||||| ||
gtgagtattgatttaataaagaaaaatt----ggaggctttcaacacagtaagttccacgtgtttttaattattaccattcatgttagaactggggactgtggagtgctttctagtgctatgacttgtttgataacaagaacatatttgtgggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGGTTCTACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATC

upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G01000.1 (Glycine max), 3'ss of exon 9
----------------------------gtaaatctgatttagtttgcaatatttttcag-aaaggtttttactcattcttgatactgctttcctcaattttggat-tcaagaaactaatatttaaatgagggtgtatt-agaaattcctgtcaaattcac---cttgctggt-------tctttttgtgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGATTTTGCTCTTGAACTACATTGGAGGGGCTACCAATCCTGGAATTTTGTC-
                            | |||  | |  |   |    || || |  || ||| |||    ||        |    | |   ||   ||||   | | |  | | | || ||  ||   |||  | |  ||   |  ||      || ||    ||| |          | ||| || |||   ||||| | ||||||||||||||||| ||  | || |||||||| ||||||||| || | |||||||| ||||||||||| ||||| ||| |||||||||  || 
gttaattgcatccacgtagccaaggagtggaaacattaggtgagtattgattttataaagcaaaagttgaggctttcaacacagtaagttccacttgtttttaattattaccatattcatgttagaactggggactgtggagtgctatctagtgctttgacaggtttgataacaagaacatatttgtgggtttgacagGAGCTATATACAGCTCATCACTATTCTCCAATCGAGCACCACCTGGAAGGGTTCTACTCTTGAATTACATTGGAGGAGCTACTAATACTGGAATTT-ATCA

upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaatctgatttagtttgcaatatttttcagaaaggtttttactcattcttgatactgctttcctcaattttggattcaagaaactaatattta-aatgagggtgtattagaaattcctgtcaaattcaccttgctggttctttttgtgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGATTTTGCTCTTGAACTACATTGGAGGGGCTACCAATCCTGGAATTTTGTC
                                                                               |   | ||  || ||| |||       |||   ||| |  |   | | ||  | ||||| ||  |  | | |||| ||||||| || |||||||| ||||| ||||| || || |||||||| ||||| |||||||| |||||||||||||| ||| |||| ||  | |||||| ||||
-----------------------------------------------------------------------------gtatatatcttgtagttataatcgtcaattatgtcaaaatgttcatagaatcttcatgctg-ttgctcgtat-ttcttcagGAACTATCTACAGCTCCTCACTCTTTCCAAATCGCGCACCGCCCGGAAGAATTTTGCTGTTGAACTACATTGGCGGGTCTACAAACACCGGAATTCTGTC

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|351045190|gb|FQ451638.1|FQ451638
EST:     TAAGGGATTTGGCCAGTTACATCCACGTAACCGAGGGGTGGAAACTTTAG                         GAACTATATACAGCTCATCACTTTTTCCTAACCGAGCACCACCTGGAAGGA
genomic: TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAGgtaaatctga ... tgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
EST: gi|352782140|gb|FQ470042.1|FQ470042
EST:     GGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTGG                         GAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
genomic: GGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAGgtaaatctga ... tgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
EST: gi|352782116|gb|FQ470018.1|FQ470018
EST:     TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAG                         GAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
genomic: TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAGgtaaatctga ... tgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
EST: gi|352764040|gb|FQ467610.1|FQ467610
EST:     TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTTG                         GAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
genomic: TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAGgtaaatctga ... tgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
EST: gi|352764188|gb|FQ471168.1|FQ471168
EST:     TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAG                         GAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
genomic: TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAGgtaaatctga ... tgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
EST: gi|351054509|gb|FQ451985.1|FQ451985
EST:     TAAGGGATTTGGCCAGTTACATCCACGTAGCCTAGGGGTGGAAACTTTAG                         GAACTATATACAGCTCATCACTTTTTCCTAACCGAGCACCACCTGGAAGGA
genomic: TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAGgtaaatctga ... tgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
EST: gi|110378936|gb|EC944096.1|EC944096
EST:     TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAG                         GAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
genomic: TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAGgtaaatctga ... tgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA
EST: gi|110381438|gb|EC934459.1|EC934459
EST:     TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAG                         GAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGAAAGGA
genomic: TAAGGGATTTGGCCAGTTACATCCACGTAGCCAAGGGGTGGAAACTTTAGgtaaatctga ... tgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtattagaaattcctgtcaaattcaccttgctggttctttttgtgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGATTTTGCTCTTGAACTACATTGGAGGGGCTACCAATCCTGGAATTTTGTC
                                    ttctttttgtgttct  CT-rich tract
     ttagaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatctgatttagtttgcaatatttttcagaaaggtttttactcattcttgatactgctttcctcaattttggattcaagaaactaatatttaaatgagggtgtattagaaattcctgtcaaattcaccttgctggttctttttgtgttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGATTTTGCTCTTGAACTACATTGGAGGGGCTACCAATCCTGGAATTTTGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG