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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcatttctcttataatttaggagagctaatatggtacttctgcaagttggttctttctggctttctaactgacaaattttgttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTTCTGGAAGACGCTATTAGGGGTGGATACCCAATCTTGATAATTGCAGAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g00240.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 6
gtttgcatttctcttataatttaggagagctaatatggtacttctgcaagttggttctttctgg---ctttctaactgaca--aattttgt-----tcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTTCTGGAAGACGCTATTAGGGGTGGATACCCAATCTTGATAATTGCAGAAG
||||| ||   |  || ||||  |   |  ||| |  || | |   | || |  |  ||| |||   || |  |  |||    ||| |||      |||   ||||||| ||||| |||||||| || |  ||||| |||||||| || |   ||||||| || |||||||||||||| ||||||||| | ||| || | || |
gtttg-atgcattctagaattcggtgtacttaa-actgtgcattaaccagatactcatttgtgggctctatgcatttgatgctaatgttgattctatcacccagTTGCTCCTTGTGGACAAGAAAATCAACAATGCCAGAGATCTTATAACAATTCTGGAGGATGCTATTAGGGGTGGGTACCCAATCCTAATAGTTACGGAGG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G065023_T01 (Zea mays), 3'ss of exon 1
gtttgcatttctcttataatttaggagagctaatatggtacttctgcaagt--tggttctttctggctttctaactgacaa--------------attttgttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTTCTGGAAGACGCTATTAGGGGTGGATACCCAATCTTGATAATTGCAGAAG
            | |||      |  | | ||| |  || | |  ||||      |||  ||     ||||  |||   ||              || ||  |  |  || ||||| | || || || || || || |||||||| ||||| || || ||| ||||||| || || || |||| |||||||||| ||||||||||||| |
----------aacctattggggggtgggggtaagacagttcctaggcaaacaacagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcagCTGCTTTTGGTTGATAATAAAATCACCAATGCAAGGGATCTTATCAACGTTTTGGAAGAAGCCATCAGAGGTGCATACCCAATCCTGATAATTGCAGAGG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtttgcatttctcttataatttaggagagctaatatggtacttctgcaagttggttctttctggctttctaactgacaaattttgttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTTCTGGAAGACGCTATTAGGGGTGGATACCCAATCTTGATAATTGCAGAAG
   ||   |||  |  || | ||    |    ||||| | |  |     |     ||  ||| || || | |  ||      | ||| |  |||||||| ||||||| ||||| |||||||||||||| |||||| | ||||   |||||||||| || ||||  |||||||||||  | ||||| ||||| ||||
gtattattattgtttatacagtt---aaatcttaata-gctgataaaaaaccgcagtattttttgactatatgtctct----tcttgcttttgtagTTGTTTCTTGTTGACAAAAAGATAACAAATGCTAGAGATATTATTAGCATTCTGGAAGATGCGATTAAAGGTGGATACCCGCTTTTGATCATTGCTGAAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttgcatttctcttataatttaggagagctaatatggtacttctgcaagttggttctttctggctttctaactgacaaattttgttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTTCTGGAAGACGCTATTAGGGGTGGATACCCAATCTTGATAATTGCAGAAG
    | | || |  | || | |    ||||||  |   |  |  ||  |      |       ||       || |||| |||      || ||||||||||||| ||||||||  |||| |||||||| |||||  ||   ||||| || || || ||||| || |||||||||||| | |||||||||||||
----gtaatttttctttattct----gagctaccaaaatgatattgtgatgcaaat------agc-------ctaacaagtttctactgtgcagTTGCTTCTTGTTGACAAGAAAGTAACCAATGCAAGGGATCTTGTTGGGGTTCTAGAGGATGCGATTAGAGGCGGATACCCAATCCTCATAATTGCAGAAG

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|351017572|gb|FQ435925.1|FQ435925
EST:     ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAG                         TTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
genomic: ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcattt ... gttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
EST: gi|110701933|gb|EE080073.1|EE080073
EST:     ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAG                         TTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
genomic: ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcattt ... gttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
EST: gi|110686609|gb|EE064441.1|EE064441
EST:     ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAG                         TTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
genomic: ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcattt ... gttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
EST: gi|110699104|gb|EE077129.1|EE077129
EST:     ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAAT-CGAGAACTGCAAG                         TTGCTTCTTGTANACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
genomic: ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcattt ... gttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
EST: gi|351036299|gb|FQ458674.1|FQ458674
EST:     ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAG                         TTGCTTCTTGTAGACCAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
genomic: ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcattt ... gttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
EST: gi|34550178|gb|CF518396.1|CF518396
EST:     ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAG                         TTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
genomic: ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcattt ... gttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
EST: gi|110713396|gb|EE089279.1|EE089279
EST:     ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAG                         TTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
genomic: ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcattt ... gttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
EST: gi|30256318|gb|CB972161.1|CB972161
EST:     ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAG                         TTGCTTCTTGTAGGCAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
genomic: ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcattt ... gttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
EST: gi|71864487|gb|DT013542.1|DT013542
EST:     ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAG                         TTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
genomic: ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcattt ... gttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
EST: gi|349815356|gb|FQ400511.1|FQ400511
EST:     ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAG                         TTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT
genomic: ACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcattt ... gttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttctgcaagttggttctttctggctttctaactgacaaattttgttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTTCTGGAAGACGCTATTAGGGGTGGATACCCAATCTTGATAATTGCAGAAG
                                         ttttgttc  CT-rich tract
                                      aaattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcatttctcttataatttaggagagctaatatggtacttctgcaagttggttctttctggctttctaactgacaaattttgttcatgtagTTGCTTCTTGTAGACAAGAAGATAACAAATGCAAGAGATCTCATTAATGTTCTGGAAGACGCTATTAGGGGTGGATACCCAATCTTGATAATTGCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA