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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatggttggatgacattgatttttcttttctttctaatttattttttcctttctcttgcctttggcttcctttccccttcttttcttttatgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTTGCCTACTTCGTTTTGAACAAAATGGTGTCTGTCAA

Basic information

species Vitis vinifera
transcript Vv14s0068g00780.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 4
-----gatggttggatgacattgatttttcttttc-tttctaatttattttttcctttctcttgcctttggcttcctttccccttcttttcttttatgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTTGCCTACTTCGTTTTGAACAAAATGGTGTCTGTCAA
       || ||  |   || |||| ||| ||||| | || | |  | | || |  ||  | |  ||| ||     |      || | |  ||||||    ||||||||||||||||||| || ||||| |||||||| || ||||| ||||||||||| ||||| || |||||||| |   | || || ||
gtactagtgattccacc-caatgatattttttttcatatccactccagtattgcaattaacgtaactt-ggaaaaatgattgtttgtgtaattttat----tgcagTCACTTCTTGCAGCTCTTGGATCGATTCAATTTGTGTCCAATATTGCATTTGCTTACTTTGTGTTGAACAAGACCATTTCAGTGAA

upper sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G477146_T01 (Zea mays), 3'ss of exon 4
gatggttggatgacattgatttttcttttctttctaatttattttttcctttctcttgcctttggcttcctttcccc--ttcttttcttttatgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTTGCCTACTTCGTTTTGAACAAAATGGTGTCTGTCAA
| |  ||   |     | ||  | |  | |  ||  ||||  | ||| |||| ||  ||   ||  ||   | |     ||  ||  ||   |||| |||||||||| |||||||| || ||||||||||| || |||||||||||||| ||||||||||| || |||||||| |   | || || ||
gcttcttacttacagctaataataccatccaatcatattt--tcttttctttttccagctagtgtttttggtacggaaattgattgtttacttgctttgcagTCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTTGCCTACTTTGTGTTGAACAAGACTATTTCAGTGAA

upper sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G144254_T06 (Zea mays), 3'ss of exon 3
gatggttggatgacattgatttttcttttctttctaatttattttttcctttct---cttgcctttggcttcctttccccttcttttcttttatgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTTGCCTACTTCGTTTTGAACAAAATGGTGTCTGTCAA
    |||   |     | ||  | |  | |  ||  ||||  ||||  ||||||   |  |  ||| | ||          |  |||  ||  |    | |||||||| |||||||| || |||||||| || || || ||||||||||| ||||||||||| ||||||||||| |   | || || ||
---tgtttcttagagctaataatgccatccaatcatattttcttttctctttctagcccagtgttttggtttgaacattgattatttacttgctatattacagTCACTACTTGCAGCTCTTGGATCAATCCAGTTTGTGTCCAACATTGCTTTTGCCTACTTTGTTTTGAACAAGACTATTTCAGTGAA

upper sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G07510.2 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------------------------------gatggttggatgacatt-----gatttttcttttctttctaatttattttttcctttctcttgcctttggcttcctttccccttcttttcttttatgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTTGCCTACTTCGTTTTGAACAAAATGGTGTCTGTCAA
                                                                                                |||||||   | |||      | | | |  ||  || | ||| ||||  |   |    || | ||||   | ||     ||| || |  | | |||||||||||||||||||||||| ||||||||  |||| || || || |||||||| || || ||||| || ||||||||||||||| | |||||
gtatgtttcccctatttaattgggattttttgttcaataatatatggtgtaaactgtaaattatgatagtatgtagtagttttgcatttttttatttggttggcatatattcggtgaaatatgcgatttcttatgattgatttaatggatgtattttcatttg---ttctgattacttattcttctgtgtgctgtgcagTCACTTCTTGCAGCGCTGGGATCTGTTCAGTTTGTATCTAACATTGCCTTCGCTTACTTTGTCTTGAACAAAATGGTGACAGTCAA

upper sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G26550.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------------------------gatggttggatgacatt-----gatttttcttttctttctaatttattttttcctttctcttgcctttggcttcctttccccttcttttcttttatgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTTGCCTACTTCGTTTTGAACAAAATGGTGTCTGTCAA
                                                                                               |||||||   | |||      | | | || ||  || | ||| ||||  |   |    || | ||||   | ||     ||| ||||  ||| |||||||||||||||||||||||| || |||||  |||| || || || |||||||| || || ||||| || ||||||||||||||| | || ||
gtatgtttcctgcaatttgattggaattttatgttcaatgatttatggtgtaattttatgataatatgtagtagttttgcagttttttttttgtttggttggtatatatttagtgaagtatgctatttcttatgattgatttgatggatgtattttcatttg---ttctgattacttatttttctttgtgctgtgcagTCACTTCTTGCAGCACTAGGATCTGTTCAGTTTGTATCTAACATTGCCTTCGCTTACTTTGTCTTGAACAAAATGGTGACAGTAAA

upper sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 4
gatggttggatgacattgatttttcttttctttctaatttattt--tttcctttctcttgcctttggcttcctttccccttcttttcttttatgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTTGCCTACTTCGTTTTGAACAAAATGGTGTCTGTCAA
  | |   |||    | ||  || | |   |   | |||| |    |||| ||    || |  || | ||   || || || |   || |    || ||||||| ||||| ||||| || ||||| |||||||| || |||||||| |||||||| ||  | || ||||||||||||||  |||||||
-gtagaatgatctgctcgacattgcctacttgcgtgatttgtcaggtttcattatggtttctctttggttttcttaccgttatgaactct----ctttgcagTCCCTTCTAGCAGCTCTTGGATCCATTCAATTTGTATCCAACATAGCATTTGCTTATGTTGTATTGAACAAAATGGTTACTGTCAA

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|161706916|gb|FC057254.1|FC057254
EST:     TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAG                         TCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
genomic: TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAGgtcagtttga ... tgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
EST: gi|351040762|gb|FQ438306.1|FQ438306
EST:     TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAG                         TCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
genomic: TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAGgtcagtttga ... tgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
EST: gi|351030030|gb|FQ430772.1|FQ430772
EST:     TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAG                         TCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
genomic: TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAGgtcagtttga ... tgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
EST: gi|351043780|gb|FQ431332.1|FQ431332
EST:     TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAG                         TCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
genomic: TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAGgtcagtttga ... tgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
EST: gi|351013510|gb|FQ425541.1|FQ425541
EST:     TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAG                         TCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
genomic: TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAGgtcagtttga ... tgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
EST: gi|37184677|gb|CF604031.1|CF604031
EST:     TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAG                         TCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT
genomic: TCTCTCTGGGAAATTGTCTTAATTTCATTTCTTTCGGATATGCTGCTCAGgtcagtttga ... tgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctttctcttgcctttggcttcctttccccttcttttcttttatgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTTGCCTACTTCGTTTTGAACAAAATGGTGTCTGTCAA
       ctcttgcctttggctt  CT-rich tract
                                ttcttttcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatggttggatgacattgatttttcttttctttctaatttattttttcctttctcttgcctttggcttcctttccccttcttttcttttatgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTTGCCTACTTCGTTTTGAACAAAATGGTGTCTGTCAA

- tggttgg