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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG

Basic information

species Vitis vinifera
transcript Vv00s0220g00010.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g41910.1 (Oryza sativa), 3'ss of exon 4
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctattt-atgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
    |  | |  ||||   || ||||   ||       || |  |        |  |   | ||| |   | |||  |||||   | |     || |  ||||||||||||||||||| ||||||||||| ||| | |||||||| |||||||| || || || || ||||| |||||||| || | ||| |||
----gtatatacaagt---aatttttgtctaagtgcttgactagttttccataagctaattctttgaaactgttaactttctttttat-----atatgtagGAAGCTAACAAACCTCCAGATAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAG

upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G084716_T01 (Zea mays), 3'ss of exon 4
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
      || || | ||  |   || |||| |          |||| |  |  |   |||  | ||| ||  | |  | |   |||||       |   ||||||||||||||||||| || |||||||| ||| | ||||| || |||||||| ||||| || || ||||| |||||||| || || || |||
------gt-tccatgtccagttttatagtcaattgactattttatgataaagctgctgg--agtta-gtagtaacctattgaacttttg-----tggtagGAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTGATGATGTCACGGTGGAGGAG

upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G411893_T01 (Zea mays), 3'ss of exon 3
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
                                    |   | |||   |    ||   |||  |   |||  || |   || | |     |   |   ||||||||||||||||||| || |||||||| ||| | ||||| || |||||||| ||||| || || ||||| |||||||| || || || |||
--------------------------------gtcaattgactat--tttatgataaagctgctggagttagtagtaacct-attgaacttttgtggtagGAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTGATGATGTCACGGTGGAGGAG

upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G171660_T02 (Zea mays), 3'ss of exon 4
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
  |   || || ||||  |   ||  ||||||   || |  ||     |    |||    | || |      || |   || | |     ||  |   ||||||||||||||||||| || |||||||| ||| | ||||| || |||||||| ||||| || || ||||| |||||||| || || || |||
-gtatagtttccaagtc-attcttggagttatttgtaagt-ttgcgcattttaattctagtcttcaataaactagtaacct-attgaacttctgtggtagGAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTGATGATGTCACAGTGGAGGAG

upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G074351_T01 (Zea mays), 3'ss of exon 4
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
        || ||  ||  ||||  |   |  | ||     |||||| |   ||  ||   |||   || || || |  |  | |     ||  |   ||||||||||||||||||| || |||||||| ||| | |||||||| |||||||| ||  | || || || || ||||||||||| || || |||
--------gtatagtttccaagtcattcatggagttct---ttataagtttgcacatgttaattctagtcttcatgtaacctattgaacttctgtggtagGAAGCTAACAAACCTCCAGACAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACATAACTGGTTTACCTGATGATGTTACAGTGGAGGAG

upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G353114_T01 (Zea mays), 3'ss of exon 7
-atttgggtgtctaagttgaaagttttagttatacttaggaatta-taactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
 |||||       | |||  | ||   |||| ||      | | | ||  |    ||   |||  |   |||  || |   || | |     |   |   ||||||||||||||||||| || |||||||| ||| | ||||| || |||||||| ||||| || || |||||  ||||||| || || || |||
tatttgaaccaaaaggttccatgtcc-agttttatagtcaattgactattttatgataaagctgctggagttagtagtaacct-attgaacttttgtggtagGAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTAATGATGTCACGGTGGAGGAG

upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 5
---------------------------------atttgggt---gtctaagttgaaagtt-ttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
                                  |||        || |  ||   | || || |||  |||| | ||| |  ||   |   | ||  |   |||     || | | |   | | | ||  || ||||||||||| ||||| |||||||||||||| || |||||  ||||||| ||||||||||| || |||||||| || ||||||||   ||| || 
gtgcgccttttctttccatcttatctatcaatggtttcaccctgatccattttcttatttcttggtttgacttggaaatgagtacct-cttctgggagacgaatggc---atctctattgatctcattctgtttcagGAAGCTAATAAACCCCCTGATAGTTGGTTTGAATTAAAGATTAATACGCATGTTTATGTCACTGGGTTGCCTGAGGATGTTACCACTGATGAA

upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G31450.1 (Glycine max), 3'ss of exon 6
---------------------------------atttgggt---gtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
                                  |||        || |  ||   | || | | | |   | ||||  || | || |  ||| |  |   |  |       | | |   | | | ||  || ||||||||||| ||||| |||||||||||||| || |||||  | ||||||||||||||||| || |||||||| || || |||||   ||| || 
gtgccccttttctttccatcttgtctatcaatggtttcaccctgatccattttcttatttcttgctttgacttggaa--atgagtacctcttttgggagacaaatggc-gcatatattgatctcattctgtttcagGAAGCTAATAAACCCCCTGATAGTTGGTTTGAATTAAAGATCAATACACATGTTTATGTCACTGGGTTGCCTGAGGACGTTACCACTGATGAA

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|110414278|gb|EC980105.1|EC980105
EST:     GCAGAGAAGAAG                         GAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACAT
genomic: GCAGAGAAGAAGgtttcacttt ... tcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
                                            ctcattt  CT-rich tract
               tatttatgtttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG