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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgaacttcttactttggacctgtaatatatctgttatttttgcaatctgtattgtgcatgtggccaggattttcatattctaacagaagatctgaaaattgtataccatgcttcctcgcgttattgcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG

Basic information

species Vitis vinifera
transcript Vv10s0003g03500.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g48270.1 (Oryza sativa), 3'ss of exon 4
gtaattgaacttcttactttggacctgtaatatatctgttatttttgcaatctgtattgtgcatgtggccaggatt-ttcatattctaacagaagatctgaaaattgtataccatgcttcctcgcgttattgcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG
                                       ||    |||  | ||    ||  ||||||||||  || |  || |  ||    ||  | |  | | |    ||||| | | || |   || ||||  |  ||||||||||||||||||||||||||||| || ||||| ||||| || ||||| |||||||| || ||||| || |||||||||||||| ||||| ||||| 
--------------------------------------gtaacactgccttttg----gtaaatgtggccagacttatctatttggtactgtaatgtatacagacttataaccataccttcttggtgtaatgccaat--agGGATATCATTCGTGGGAGTCCAGATGTCAAATGGGAAAGCATTAAAGGTTTGGAGAATGCAAAGCGTCTTCTGAAAGAAGCAGTTGTGATGCCTATAAAA

upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 4
gtaattgaacttcttactttggacctgtaatatatctgttatttttgcaatctgtattgtgcatgtggccaggattttcatattctaacagaagatctgaaaattgtataccatgcttcctcgcgttattgcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG
                                              | |||      |   ||      |   |     |||    | || || || ||   ||||   || ||   | || || ||     || | |||||| || ||||| || |||||||||||||| ||||| |||||||| ||  | |||||||||||||| || || ||||| |||||||||||||| ||||||
----------------------------------------------gtaattcaagattcacaaactttcgaaaa----ataggaaagcacaa-atttggccattg---actatatattcttgcctt--catct-ttcagGGACATTATTCGCGGCAGTCCAGATGTGAAATGGGAAAGCATCAAAGGACTGGAGAATGCCAAACGCCTTCTAAAAGAGGCAGTTGTCATGCCCATAAAG

upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G115766_T02 (Zea mays), 3'ss of exon 3
gtaattgaacttcttactttggacctgtaatatatctgttatttttgcaatctgtattgtgcatgtggccaggattttcatattctaacagaagatctgaaaattgtataccatgcttcctcgcgttattgcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG
                                  |    | |||    ||||||||     ||||    ||  | |    || | |||   |   || ||    ||| ||| ||   | |   |   | |||||   ||||||||| |||||||| ||||||||||| || ||||| ||||| || ||| | |||||||| || ||||| || |||||||||||||| |||||||| || 
---------------------------------gtaaactgtttcaa-aatctgta-----catgacatcaatagtgcggtactgtaatgtattctc-gactgctgt-tactatagcttccttctccaatgccta--cagGGATATAATTCGTGGAAGTCCAGATGTTAAATGGGAAAGCATAAAAGGTCTGGAGAATGCAAAGCGTCTTCTCAAAGAAGCAGTTGTAATGCCAATTAAA

upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 4
gtaattgaacttcttactttggacctgtaatatatctgttatttttgcaatctgtattgtgcatgtggccaggattttcatattctaacagaagatctgaaaattgtataccatgcttcctcgcgttatt-gcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG
                                                     ||| | |  |  |      |  ||| | ||||    |     |     |  ||| |   |   ||  || | | ||| | |  | ||||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||  | || ||||| ||||| || || ||||| || ||||||||||| ||||||
-----------------------------------------------------gtaatctaaacatcattgtggctttaacattcagggacggtgtggtctagctgt-tgaaacattttatcccatcatttggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACTGGAAAATGCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAG

upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 4
gtaattgaacttcttacttt----ggacctgtaatatatctgttatttttgca-atctgtattgtgcatgt-ggccaggattttcatattctaacagaagatctgaaaattgtatac-catgcttcctcgcgttattgcctgtcc-agGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG
|||| |   ||    |  |       |||| | ||| | ||| |   |      |   ||  | ||  ||| || || ||||||||| |   ||   |   |||| || ||  ||   |||   |  | |  | |||||   ||  ||||||||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||||||| | || ||||| || ||||| ||||| || |||
gtaaattttctctcaatctcttcaacacctctgatagaactgatgactacatggagaagttatttgtgtgttggtcaagattttcatgtgtgaatctat--tctgtaagtttaattttcatatatgtttg--tcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTACTGAAAGAGGCTGTTGTGATGCCGATTAAG

upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G26100.1 (Glycine max), 3'ss of exon 4
gtaattgaacttcttacttt----ggacctgtaatatatctgttatttttgca-atctgtattgtgcatgt-ggccaggattttcatattctaacagaagatctgaaaattgtataccatgcttcctcgcgttattgcctgtcc-agGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG
|||| |   ||    |  |       ||||   ||| | |   |   |      |    |  | ||||||| || || ||||||||| |  |   |     |||| || ||  ||    |  |   |   || |||||   ||  ||||||||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||||||| |  | ||||| || ||||| ||||| || |||
gtaaattttctctcaatctcttcaataccttggatagaaccaatgactacatggagaaattatttgcatgttggtcaagattttcatgtgattctat----tctgtaagttcaattttcttatatgtt-tgtcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTATTAAAAGAGGCTGTTGTGATGCCGATTAAG

upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattgaacttcttactttggacctgtaatatatctgttatttttgcaatctgtattgtgcatgtggccaggattttcatattctaacagaagatctgaaaattgtatacc-atgcttcctcgcgttattgcctgtc-cagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG
                                                     |||  ||   |||||| |    |   ||||| |  |        || | ||  | | |   |  ||  |   |   | |  |||  |||||||||||| ||||||| |||| || | |||||||| |||||||| ||||| ||||| || |||    |||| |||||||| || || ||||| ||||| 
-----------------------------------------------------gtaa-gtcattgtggcta---ctgatatatttttgct-----cttggacatcatgttcttgttttttttgatgaactggtgtgtttcagGGATATCATCCGTGGGAATCCAAATATCAAGTGGGAAAGCATCAAAGGTTTGGAGAACGCTAAAAAGTTGCTCAAAGAAGCTGTGGTGATGCCTATAAAA

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|27586367|gb|CB009062.1|CB009062
EST:     CCTTCTTTTGAGTCTGCTGACATGCGTGCCTTAGGGGAGAGTTTAAGTAG                         GGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTT
genomic: CCTTCTTTTGAGTCTGCTGACATGCGTGCCTTAGGGGAGAGTTTAAGTAGgtaattgaac ... gcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTT
EST: gi|37184610|gb|CF603964.1|CF603964
EST:     CCTTCTTTTGAGTCTGCTGACATGCGTGCCTTAGGGGAGAGTTTAAGTAG                         GGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTT
genomic: CCTTCTTTTGAGTCTGCTGACATGCGTGCCTTAGGGGAGAGTTTAAGTAGgtaattgaac ... gcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTT
EST: gi|110732627|gb|EE108077.1|EE108077
EST:     CCTTCTTTTGAGTCTGCCGACATGCGTGCCTTAGGGGAGAGTTTAAGTAG                         GGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTT
genomic: CCTTCTTTTGAGTCTGCTGACATGCGTGCCTTAGGGGAGAGTTTAAGTAGgtaattgaac ... gcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTT
EST: gi|37189203|gb|CF608552.1|CF608552
EST:     CCTTCTTTTGAGTCTGCCGACATGCGTGCCTTAGGGGAGAGTTTAAGTAG                         GGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTT
genomic: CCTTCTTTTGAGTCTGCTGACATGCGTGCCTTAGGGGAGAGTTTAAGTAGgtaattgaac ... gcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacagaagatctgaaaattgtataccatgcttcctcgcgttattgcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG
 ttctaac  putative branch site (score: 1)
                                              cctgtcc  putative PPT
              aaaattgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgaacttcttactttggacctgtaatatatctgttatttttgcaatctgtattgtgcatgtggccaggattttcatattctaacagaagatctgaaaattgtataccatgcttcctcgcgttattgcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC