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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG

Basic information

species Vitis vinifera
transcript Vv06s0004g00180.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 2
---------------------------gatcaacatctt-----aaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatga----tgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG----------------------------
                             |||   ||||     |||      |  | |         | | |    ||    | | |     || |  | | | || | ||| | ||| |    || ||   |||||||||||||| || ||||||||||||||||||||||| || || ||  ||||||||||||| |||||||||                            
gtatagcttcagcttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
  |  |    || ||  | |  |  | |       | |  ||   | |  ||||| ||  | || | |||  || |  ||| |      |       |||||||||||||| || |||||||| ||||| || |||||||| || ||| |||||||||| || || || |||
cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 2
-gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
 |  ||      | |     |  ||||       ||   ||  |      ||     ||  |  | | |||  || |  ||| |      |   |   |||||||||||||| || |||||||| ||||| || || ||||| || ||| |||||||||| || || || |||
tgcacactgaggttatagcatctctatctactccatccgttc-caaaatataagcactgtaatatatgttttagtttgctaactcctcttttcacaaacagCGTTTTGCTGCAGTTATCATGAGAATAAGAGAACCGAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 2
gatcaacatcttaaccttgttcctattgga----ggaattttttttctttccctatttgttgccagttttttt--tatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
      |||  |  | |||||   |||  |    | |      |   |||  || | | ||  ||||| || |  | ||||| || | | | | || |     |||||||||||||| ||||||||||| ||||| || || |||||||||||  |||||||||| || || || |||
------cattctttctttgttatgattatataatgtagcaacctgatttttgctgtgttttctcagttattatattttgtatgttgactcttttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G092916_T01 (Zea mays), 3'ss of exon 2
gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG----------------------------
                                                  ||||| |  | |   | |    ||       ||   |  |       |||||||||||||| |  ||||||||||||||||| || || || ||| |  ||||||||||||| || ||||||                            
----------------------------------------------ttacatttgatatctgcagtctcagcgtgaccctgatacttact----tgacagCGTTTTGCTGCGGCTATCATGAGGATAAGGGAGCCCAAGACAACGACACTGATATTTGCTTCAGGGAAGATGGTCTGCACCGGAGCAAAGAGCGAAGCCG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
gatcaacatcttaaccttgttcctattggaggaattttttttctttcccta--tttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
  ||    |  | |   |  |  |||      |  |  |  | ||| |  |  ||| |  | | | || | | | ||| || |   | | || |     |||||||||||||| || |||||||| ||||| || || |||||||| ||  |||||||||| || || || |||
--tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctctattattatatttttatcttgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G04500.2 (Glycine max), 3'ss of exon 2
gatcaacatcttaaccttgttcctattggaggaatttttttt--ctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
  |    ||    |     |   ||    | | ||| |      |  | |  ||| ||||   || |  | ||   || ||     | || | |   |||||||||||||||| || || ||||||||||| || || ||||| || ||| | || ||||||||||| ||||||
-cttgctattcagaatcattaattagcaaatgtattatacacgccagttctaattggttggtggtatactgtactgatgtttgtgatgtgtt-tgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
----gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
         | |||   |  |  ||   ||   ||  || | |||    | |  ||| ||      | |    |   ||| |  |  || |||  |   |||||||||||||||| || || |||||||| ||||| |||||||| || ||  | || ||||| ||||| ||||||
ttttatctgagatcaataattaatttgcatgctagacatgtcttta---tgctgattggtcatttatctgcagtgcttatgtctatcttttga-atctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 3
----gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
         | |||   |  |  ||   ||   ||  || | |||    | |  ||| ||      | |    |    || |  |   | |||  |   |||||||||||||||| || || |||||||| ||||| |||||||| || ||  | || ||||| ||||| ||||||
ttttatctgagatcaataattaatttgcatgctagacatgtcttta---tgctgattggtcatttatctgcactgctaatgtctatcatttga-atctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 3
gatcaacatcttaaccttgtt--cctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
  ||      |     |  ||    |   |  | | | ||| | ||    ||| | ||||   || |  | ||   || |      | || | |   |||||||||||||||| || || ||||||||||| || || ||||| || ||  | || ||||||||||| ||||||
-ttctgttattcggaatcattaatttgcagatgtattatttgtgctagttctaatggttggtggtatgctgtactgatgtctgtgatgtgtt-tggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTTATTTTTGCTTCTGGCAAGATG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 3
-------gatcaacatcttaaccttgttcc--tattggaggaattttttttctttccctatttgttgccagtttttttt-atgtattttaaatttatgatgt-tcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
         ||    |  ||  | ||||    || | ||  | ||| |||  | |||     | | |   || ||||   || |  ||| ||| | || | | |  | |||||||| ||||| |||||||||||||| || || ||||| ||||| || || || ||||||||||| || |||
gttttgctttctttgtgatattcgtgttttagtaatcgatcattttgtttggtctccaccactttggtttgtattttcggatttggttttaatctgtgttttatgttccagCGTTTCGCTGCTGTAATCATGAGGATCAGAGAGCCAAAGACCACAGCGTTAATTTTTGCTTCTGGGAAAATG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ29072 (Selaginella moellendorffii), 3'ss of exon 2
gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
                                    ||| ||  |   || ||| || |   | | |||||||  || |   | | |  | ||    |||||||||||||| || |||||| | ||||| || || |||||||||||| | || ||||| || |||||||||
-----------------------------------gtttgtttgtgttctttttttttctcttgtgttttatgacttgtctctctcttctcttatc-cagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
                                   ||| ||| | | | | ||| |  |  |||||| | |  | | |     |        |  | |||||||||||||| || |||||| | ||||| || || |||||||||||| | || ||||| || |||||||||
----------------------------------gtttgtttgtgttcttttttttctcttgtttttatgacttgtctctctctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG

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|161713889|gb|FC062573.1|FC062573
EST:     ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG                         CGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
genomic: ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAGgtatgctaac ... gttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
EST: gi|349817400|gb|FQ405404.1|FQ405404
EST:     ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGTAGAATACAATCCAAAG                         CGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
genomic: ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAGgtatgctaac ... gttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
EST: gi|30304500|gb|CB981294.1|CB981294
EST:     ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG                         CGTTTTGCTGCCGTAATCAT
genomic: ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAGgtatgctaac ... gttcctgcagCGTTTTGCTGCCGTAATCAT
EST: gi|110721938|gb|EE097741.1|EE097741
EST:     ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG                         CGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
genomic: ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAGgtatgctaac ... gttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
EST: gi|71881466|gb|DT030521.1|DT030521
EST:     ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG                         CGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
genomic: ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAGgtatgctaac ... gttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
EST: gi|110724394|gb|EE100183.1|EE100183
EST:     ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG                         CGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
genomic: ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAGgtatgctaac ... gttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
EST: gi|71881168|gb|DT030223.1|DT030223
EST:     ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG                         CGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG
genomic: ATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAGgtatgctaac ... gttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
                                            tgttcct  CT-rich tract
               agttttttttatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- -caacatc
- - - - - - - - - - -cctattg