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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaactaagaacatctttaatgttttcttatttagctggtgcatgattgatcagttacattttattcagcttgaatcttgctgacttactgtctaagacatttcattaaaatgacttgttggtttactctaatgcttgcttatggttacag

Basic information

species Vitis vinifera
transcript Vv08s0007g01980.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G368908_T03 (Zea mays), 5'ss of exon 1
---CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaactaagaaca----tctttaatgtttt-cttatttagctggtgcatgattgatcagttacattttattcagcttgaatcttgctgacttactgtctaagacatttcattaaaatgacttgttggtttactctaatgcttgcttatggttacag
    |||||||| || |||||| |||| || |||||||| ||||| |||||||| || || ||||||||||| ||||| || || || ||||| ||||||||| |      | |       ||  | |||||  |||  ||     |||  | ||   |  ||| |  ||    |||                                                                                  
CAGTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCTTGGGATACCCACCAAGGCGTATTACGCCGTGGAAGAAGTTAAAGAGgtatgtctgggggatgagatgctggagtgtttcacttgcttgctcagtgtttaatatttttgttgcccttc--ccag----------------------------------------------------------------------------------

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 4
CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaactaagaacat----ctttaatgtttt-cttatttagctggtgcatgattgatcagttacattttattcagcttgaatcttgctgacttactgtctaagacatttcattaaaatgacttgttggtttactctaatgcttgcttatggttacag
 |||||||| || |||||| |||| || |||||||| ||||| |||||||| || || ||||||||||| ||||| || || || ||||| ||||||||| |      | |       ||  | |||||  |||  ||     |||  | ||   |  ||| |  ||    |||                                                                                  
TTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCTTGGGATACCCACCAAGGCGTATTACGCCGTGGAAGAAGTTAAAGAGgtatgtctgggggatgagatgctggagtgtttcacttgcttgctcagtgtttaatatttttgttgcccttc--ccag----------------------------------------------------------------------------------

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 4
CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgta-agaactaagaacatctttaatgttttcttatttagctggtgcatgattgatcagttacattttattcagcttgaatcttgctgacttactgtctaagacatttcattaaaatgacttgttggtttactctaatgcttgcttatggttacag
 |||||||| ||||| ||||| || || |||||||||||||| |||||||| || || || ||||| || || || ||||| ||||| || ||||||||| | ||||       |   |   ||||| | | ||   || |   || || ||  |||   |  | | |||                                                                                  
TTATGTTCCTAATCCAGTCTTGGTGATTATTGATGTCCAACCCAAGGAGCTGGGTATACCGACCAAAGCGTACTACGCTGTGGAGGAGGTTAAAGAGgtacataacttgctgagttgctggagtttt-tcacttgcttgctcagtgtttaatttgttttttcctttacag----------------------------------------------------------------------------------

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 4
CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaactaagaacatctttaatgttttcttatttagctggtgcatgattgatcagttacattttattcagcttgaatcttgctgacttactgtctaagacatttcattaaaatgacttgttggtttactctaatgcttgcttatggttacag
||| ||||| ||||| || || ||||| |||||||||||||| || || || ||||| ||||| || || || ||||| |||||||| |||||||||||||  || |   |  | | |||         ||||  ||  |||  || || | |||| ||| | |   | ||||| |       |||| |||  | ||  ||   ||  | ||  ||  |||  ||  ||  |  |||   | |   | |||
CTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGgtgaaagaggtaaataccagccaattttctaac-------cattttact--tgctcgactgttaagttgcatctgacata-cttgattt------actttctgcattagttat---atccatatatctaattgccttgatccga-acttctctct--ctgcag

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|161713904|gb|FC062870.1|FC062870
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCCACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|110689439|gb|EE065663.1|EE065663
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|110409702|gb|EC975372.1|EC975372
EST:     CTAGGAATTCCCACCCAAGGCTTATTATGCTG-TGAGGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: CTAGGAATTCCCA-CCAAGGCTTATTATGCTGTTGA-GGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|110697690|gb|EE074900.1|EE074900
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|33406800|gb|CF212427.1|CF212427
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|30297109|gb|CB973903.1|CB973903
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCCACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|33409710|gb|CF215337.1|CF215337
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCCACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|71864815|gb|DT013870.1|DT013870
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTG
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTG
EST: gi|294967321|gb|GW836675.1|GW836675
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|110713466|gb|EE089412.1|EE089412
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAANAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|110711679|gb|EE088432.1|EE088432
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|71859938|gb|DT008993.1|DT008993
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCCAGAAAAGCCAGAAGGT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCC-AGAAAAGCCAGAAGGT
EST: gi|110687327|gb|EE064641.1|EE064641
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|161712650|gb|FC062222.1|FC062222
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCCACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCC
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCC
EST: gi|110718297|gb|EE094970.1|EE094970
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAAGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|30321841|gb|CD005103.1|CD005103
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|71864932|gb|DT013987.1|DT013987
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|29783602|gb|CB349901.2|CB349901
EST:     AGCTGGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|18459292|gb|BM437570.1|BM437570
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|110732758|gb|EE108326.1|EE108326
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|110690336|gb|EE067344.1|EE067344
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|33406603|gb|CF212230.1|CF212230
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|110396200|gb|EC961881.1|EC961881
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCCACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|110401013|gb|EC967604.1|EC967604
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|161721407|gb|FC070435.1|FC070435
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
EST: gi|110712994|gb|EE088527.1|EE088527
EST:     AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG                         AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT
genomic: AGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaacta ... atggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAGgtaagaactaagaacatctttaatgttttcttatttagctggtgcatgattgatcagttacattttattcagcttgaatcttgctgacttactgtctaagacatttcattaaaatgacttgttggtttactctaatgcttgcttatggttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT