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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaagccatgtgtttatgtctccttctctttcttttcaaagtttgttgttccctctctatttcttattgcataatcgttgtccatctcctttgttacagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTTCCTAGTGTCAACAAG

Basic information

species Vitis vinifera
transcript Vv07s0141g00220.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0141g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G34360.1 (Glycine max), 3'ss of exon 2
------ttgaagccatgtgttt--atgtctccttctctttcttttcaaagtttgttgttccctctctatttcttattgcataatcgttgtccatctcctttgttacagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTTCCTAGTGTCAACAAG
      || |||  || || ||  |||     |  | |         |||||||| | ||  | | | || | | || |            ||| ||     ||||||||||||||||||||||||||||| ||||| || ||| |||| ||||| ||||| ||||||||||||
gtgagctttaagatatttgcttgaatgcaaattgttttgctggggttaagtttgtagctcattttgtcttccatgttac------------catttc----attacagTTACGCAGAGAAAGAATAGCAGAAAGAATCAGGGCATTGCAAGAACTGGTTCCAAGTGTCAACAAG

upper sequence: Vv07s0141g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G31510.1 (Glycine max), 3'ss of exon 2
ttgaagccatgtgtttatgtctccttctctttcttttcaaagtttgttgttcc-ctctctatttcttattgcataatcgttgtccatctcctttgttacagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTTCCTAGTGTCAACAAG
          |||  |  |  |     | ||| |  |  ||   |   | ||| | |   ||  || |||   |  ||  |||  |  |  ||  |||||||| |||||||||||||||||||| ||||| || ||| |||| ||||| ||||| ||||||||||||
----------gtgagtgagctttaagatatttttgcttgaatgctacagatccacacagcatagctcattttgtcttccatgttaacgtt-ttcattacagTTGCGCAGAGAAAGAATAGCAGAAAGAATCAGGGCATTGCAAGAACTGGTTCCAAGTGTCAACAAG

upper sequence: Vv07s0141g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G03690.1 (Glycine max), 3'ss of exon 2
-----------------ttgaagccatgtgtttatgtctccttct-ctttcttttcaaagtt-tgttgttccctctctatttcttattgcataatcgttgtccatctcctttgtt-----------acagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTTCCTAGTGTCAACAAG
                    |    |  |  ||   | |  |  | |||  | |||||| || ||       | |  ||||| |||||   ||||   | |  ||      ||||           |||||| |||||||| ||||||||||| ||||| || ||  |||| ||||| || |||||||||||||||
gtgggcactagatatttccaagaatacatactttcttattatggtgcttaatattcaaaattatgacaaaatcacgttattttttattagctaatttgtttttattcttcatgtttccgttcaatgacagTTGCGCAGAGAGAGAATAGCAGAAAGAATCAGGGCTTTGCAAGAACTGGTCCCTAGTGTCAACAAG

upper sequence: Vv07s0141g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G16110.1 (Glycine max), 3'ss of exon 2
------------------------------ttgaagccatgtgtttatgtctccttctctttcttttcaaagtttgttgttccctctctatttcttattgcataatcgttgtccatctcc----tttgttacagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTTCCTAGTGTCAACAAG
                               |     | |||  |  ||  |  |  |||   || | | ||  |    ||   | | ||||   || |  ||  |  || | ||| |      ||  | |||||| |||||||| ||||||||||| ||||| || ||  |||| ||||| || |||||||||||||||
gtgggcactggatatttccaagattacagactttcttcttgttatggtgcttaatattctaaattatgacagaatcacattatttttttattatataatttatttttatttttcatgtttccgtttaatgacagTTGCGCAGAGAGAGAATAGCAGAAAGAATCAGGGCTTTGCAAGAACTGGTCCCTAGTGTCAACAAG

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|30303738|gb|CB980532.1|CB980532
EST:     TGCGGGCGAGACGTGGACAGGCCACAGATCCACACAGCATTGCTGAGCGG                         TTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTT
genomic: TGCGGGCGAGACGTGGACAGGCCACAGATCCACACAGCATTGCTGAGCGGgtaagcttga ... tttgttacagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTT
EST: gi|294965144|gb|GW836975.1|GW836975
EST:     TGCGGGCGAGACGTGGACAGGCCACAGATCCACACAGCATTGCTGAGCGG                         TTACGCAGAGAAAGAATAGCAG
genomic: TGCGGGCGAGACGTGGACAGGCCACAGATCCACACAGCATTGCTGAGCGGgtaagcttga ... tttgttacagTTACGCAGAGAAAGAATAGCAG
EST: gi|32459553|gb|CD800727.1|CD800727
EST:     TGCGGGCGAGACGTGGACAGGCCACAGATCCACACAGCATTGCTGAGCGG                         TTACGCAGAGAAAGAATAGCAGAGAGAATTGGAGCACTGCAGGAACTAGTT
genomic: TGCGGGCGAGACGTGGACAGGCCACAGATCCACACAGCATTGCTGAGCGGgtaagcttga ... tttgttacagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTT
EST: gi|34549352|gb|CF517584.1|CF517584
EST:     TGCGGGCGAGACGTGGACAGGCCACAGATCCACACAGCATTGCTGAGCGG                         TTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTT
genomic: TGCGGGCGAGACGTGGACAGGCCACAGATCCACACAGCATTGCTGAGCGGgtaagcttga ... tttgttacagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTT
EST: gi|34549438|gb|CF517670.1|CF517670
EST:     TGCGGGCGAGACGTGGACAGGCCACAGATCCACACAGCATTGCTGAGCGG                         TTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTT
genomic: TGCGGGCGAGACGTGGACAGGCCACAGATCCACACAGCATTGCTGAGCGGgtaagcttga ... tttgttacagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttccctctctatttcttattgcataatcgttgtccatctcctttgttacagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTTCCTAGTGTCAACAAG
                                 ttgtccatctccttt  CT-rich tract
             tatttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaagccatgtgtttatgtctccttctctttcttttcaaagtttgttgttccctctctatttcttattgcataatcgttgtccatctcctttgttacagTTACGCAGAGAAAGAATAGCAGAGAGAATTAGAGCACTGCAGGAACTAGTTCCTAGTGTCAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - -catgtgt
- - - - - - - - - - - ccttctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatctc