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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcatcattaatcaacctatttatatctcttctattcctcttggggatccatttacaactgtggtggaagtaactattgggtctcatatttacagGGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAGCCAGATGTCTCTAAACATGAAATGGATGCCCAAGCAGCATTGAAGCCAT

Basic information

species Vitis vinifera
transcript Vv16s0022g02320.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 20
---------gtaggcatcattaatcaacctatttatatct-----cttctattcctcttggggatccatttacaactgtggtggaagtaactattgggtct-catatttacagGGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAGCCAGATGTCTCTAAACATGAAATGGATGCCCAAGCAGCATTGAAGCCAT
          |  |  |  ||   || | | |   | ||       ||  || | ||||||  ||| |   | ||      |  |||| | |  ||  | |   | ||||||||| || ||||||||||| |||||||||||| | || |||||||||||||| ||||||||||||||||||||  | ||||| |||   || || || ||||
gtatgtggaatctgtttgtttgtccaccttgtccctttcaaagaagttgaatccatcttggaaatctacgcataa----aatttaagtcagtgctgtttttatttttttacagGGTACTGGTTCTGCAGGGGCAACTGTTAGAGTGTACATTGAACAGTTTGAACCAGATGTCTCTAAACATGATGTTGATGCTCAAATTGCCTTAAAACCAT

upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 20
gtaggcatcattaatcaacctattta---tatctcttcta-----------ttcctcttggggatcca--tttacaactgtggtggaagtaac---------tattgggtctcatatttacagGGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAGCCAGATGTCTCTAAACATGAAATGGATGCCCAAGCAGCATTGAAGCCAT
||| |   ||||  |     | |  |   | || |||  |           | | ||||||  ||| |    || || |    |    |  |          | ||   | || | |||||||||||| ||||||||||| || || |||||| | || |||||||||||||| ||||||||||||||||||||  | ||||| |||   || || || ||||
gtatgtggcatttgtttgtttgtccaccttgtcgctttcaaagaagttgaatccatcttggaaatctaggcgtaaaattaaattcattgctatcttttttctttttctttttcttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAACCAGATGTCTCTAAACATGATGTTGATGCTCAAATTGCCTTAAAACCAT
















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|351031398|gb|FQ445423.1|FQ445423
EST:     GTGTTCGATTTGTTTTTACGGATGGATCAAGGATCATATATCGTTTATCA                         GGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAG
genomic: GTGTTCGATTTGTTTTTACGGATGGATCAAGGATCATATATCGTTTATCAgtaggcatca ... atatttacagGGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAG
EST: gi|110429629|gb|EC996127.1|EC996127
EST:     GTGTTCGATTTGTTTTTACAGATGGATCAAGGATCATATATCGTTTATCA                         GGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAG
genomic: GTGTTCGATTTGTTTTTACGGATGGATCAAGGATCATATATCGTTTATCAgtaggcatca ... atatttacagGGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAG
EST: gi|32249648|gb|CD715467.1|CD715467
EST:     GTGTTCGATTTGTTTTTACAGATGGATCAAGGATCATATATCGTTTATCA                         GGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAG
genomic: GTGTTCGATTTGTTTTTACGGATGGATCAAGGATCATATATCGTTTATCAgtaggcatca ... atatttacagGGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggggatccatttacaactgtggtggaagtaactattgggtctcatatttacagGGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAGCCAGATGTCTCTAAACATGAAATGGATGCCCAAGCAGCATTGAAGCCAT
                           aagtaac  putative branch site (score: 2)
                                           tcatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcatcattaatcaacctatttatatctcttctattcctcttggggatccatttacaactgtggtggaagtaactattgggtctcatatttacagGGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAGCCAGATGTCTCTAAACATGAAATGGATGCCCAAGCAGCATTGAAGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC