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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaaaaaccaacatatttcacatctctttctcatatcatccactggacttgacaaattgtcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATTGGCAAGATATTGAAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04590.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g51100.1 (Oryza sativa), 3'ss of exon 5
-------------gtaaggaaaaac-caacatatttcacatctctttctcatatcatccactg-gacttgacaaattgtcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATTGGCAAGATATTGAAG
              || |  ||  | |||   | | || | | |    ||| || ||   ||  || ||| |      |||| ||||||| |||||||| ||  | || ||||| ||||||||| |||||||||||||||| ||||| ||||||
gtaactatcctatatatgtgaatccacaattgactccata-cgcacattcacattattacctatgatttgtct--ccctcatcaacagGGCCATACACTCCGTTTATTATCCTTGCCAGATTTCCTGGATGCATCTATTGGGAAGATCTTGAAG

upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 5
gtaaggaaaa-accaacatatttcacatctc---tttc--------tcatatcatccactggacttgacaaattgtcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATTGGCAAGATATTGAAG
||||  |    ||||   | | ||| || |    | |         ||| || |||  ||    ||  | || | || || |||||| |||||||| ||| | || ||||| ||||||||||||||||| || ||||| || || ||||||
gtaataaccctaccattgtgtatcaaatgttgaatctacatgggagtcacattatcagctattattcgctaact-tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG

upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G35320.1 (Glycine max), 3'ss of exon 6
-------gtaaggaaaaaccaacatatttca---catctctttctcatatcatccactggacttgacaaattgtcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATTGGCAAGATATTGAAG
         |||   | |   | ||||||||   || || | | |  || |||    | |  || |   ||  |  |||||||||||| ||| | ||  | ||||||||||| ||||||||||||||||| ||||| |||||| |||||
gtgagcaaaaagatgatagttatatatttcagatcacctttgttttttagcatttcataggatttatgcatgttacttaacagGGTCACACATTACGATTATTGTCCTTACCCGATTTCTTGGATGCATCCATTGGGAAGATACTGAAG

upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 6
-------gtaaggaaaaaccaacatatttcacat---ctctttctcatatcatccac-tggacttgacaaattgtcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATTGGCAAGATATTGAAG
         |||   | |   | |||||||||||   || | | | ||| |||   | | |  || ||| ||  ||   |||||||||| ||| | ||  | ||||||||||| ||||||||||||||||| ||||| |||||| |||||
gtgagcaaaaagctgatagttatatatttcacatcacctttgttttataacattatcataggatttacacatgttcccaaacagGGTCACACATTACGATTATTGTCCTTACCCGATTTCTTGGATGCATCCATTGGAAAGATACTGAAG

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|349820813|gb|FQ404198.1|FQ404198
EST:     CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACG                         GGTCATACACTGCGGCTTTTTTCCTTACCA
genomic: CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACGgtaaggaaaa ... tcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCA
EST: gi|349812310|gb|FQ406331.1|FQ406331
EST:     CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACC                         GGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGA
genomic: CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACGgtaaggaaaa ... tcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGA
EST: gi|349827879|gb|FQ422747.1|FQ422747
EST:     CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACG                         GGTCATACACTGCGGCTTTT
genomic: CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACGgtaaggaaaa ... tcattaacagGGTCATACACTGCGGCTTTT
EST: gi|349822994|gb|FQ399973.1|FQ399973
EST:     CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACG                         GGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATT
genomic: CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACGgtaaggaaaa ... tcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATT
EST: gi|351025874|gb|FQ427886.1|FQ427886
EST:     CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACG                         GGCCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATT
genomic: CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACGgtaaggaaaa ... tcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATT
EST: gi|351029701|gb|FQ427541.1|FQ427541
EST:     CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACG                         GGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATT
genomic: CACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACGgtaaggaaaa ... tcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcacatctctttctcatatcatccactggacttgacaaattgtcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATTGGCAAGATATTGAAG
                                acttgac  putative branch site (score: 4)
                  atatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaaaaaccaacatatttcacatctctttctcatatcatccactggacttgacaaattgtcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATTGGCAAGATATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG