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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttaattccaacaccaagacctcatttgaccggcactgaatggataatttcataattttttggcattttgtaaggctaatctcacatacaatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTACCTGTCCTCCTTGTCATTTCTCAGTATGTTTCAATGGAGCTGATGAAGC

Basic information

species Vitis vinifera
transcript Vv06s0004g04460.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G14960.1 (Glycine max), 3'ss of exon 6
-tctta-attccaacaccaagacctcatttgaccggcactgaatggataatttcataattttttggcattttgtaaggctaatctcacatacaatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTACCTGTCCTCCTTGTCATTTCTCAGTATGTTTCAATGGAGCTGATGAAGC
 | ||  | ||     ||||||    ||         |||   |  ||   ||    | | |    |||| |  |    ||| |  |||| |  || | ||||| || |||||||| ||||| |||||||| ||||||||||| |||||||||||| | || |||||| ||||||| || |||||||||||  | ||||| |
ttgttgcagtcatgttccaagaggaaataaatggaaaactttgtaaattgattttgtactctaaatcattatacagtcataa-caaacat-cggtcatgcagGACGGGCATCCACCTTTGGGTTGGCAAGATACTGCAGCATATCTTGTTTTACCTATTCTTCTTGTCGTTTCTCAATACGTTTCAATGGAAATCATGAAAC

upper sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G06920.1 (Glycine max), 3'ss of exon 6
tcttaattccaacaccaagacctcatttgaccggcactgaatggataatttcataattttttggcattttgtaaggcta-atctcacatacaatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTACCTGTCCTCCTTGTCATTTCTCAGTATGTTTCAATGGAGCTGATGAAGC
 ||  | ||     ||||||    ||         |||   |  ||   ||    | |||    |||| |  |     | | |  |||| |  |  | ||||| || |||||||| ||||| |||||||| ||||||||||| |||||||||||| | || |||||| ||||||| || |||||||||||  | ||||| |
gctgcagtcatgttccaagaggaaataaatggaaaacttcgtaaattgattttgtactttaaatcattatacagtatcataacaaacat-ctgttatgcagGACGGACATCCACCTTTGGGTTGGCAAGATACTGCAGCATATCTTGTTTTACCTATTCTTCTTGTCGTTTCTCAATACGTTTCAATGGAAATCATGAAAC
















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|349809519|gb|FQ414409.1|FQ414409
EST:     TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTG                         GATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
genomic: TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTGgtaatcaaaa ... aatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
EST: gi|349824427|gb|FQ417814.1|FQ417814
EST:     TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTG                         GATGGCCATCCAC
genomic: TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTGgtaatcaaaa ... aatcctacagGATGGCCATCCAC
EST: gi|351022475|gb|FQ446997.1|FQ446997
EST:     TGCTGCTCGACAAAGTGGATCTGGCATTTTCT-GGCTTATTCCGTTTGTG                         GATGGGCATCCACCATTG
genomic: TGCTGCTCGACAAAGTGGATCTGGCATTT-CTTGGCTTATTCCGTTTGTGgtaatcaaaa ... aatcctacagGATGGCCATCCACCATTG
EST: gi|18458571|gb|BM436849.1|BM436849
EST:     TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTG                         GATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
genomic: TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTGgtaatcaaaa ... aatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
EST: gi|30327231|gb|CD010493.1|CD010493
EST:     TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTG                         GATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
genomic: TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTGgtaatcaaaa ... aatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
EST: gi|32269560|gb|CD718719.1|CD718719
EST:     TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTG                         GATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
genomic: TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTGgtaatcaaaa ... aatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
EST: gi|352799049|gb|FQ480898.1|FQ480898
EST:     TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTG                         GATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
genomic: TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTGgtaatcaaaa ... aatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
EST: gi|110374436|gb|EC939192.1|EC939192
EST:     TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTG                         GATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
genomic: TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTGgtaatcaaaa ... aatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
EST: gi|33402160|gb|CF207787.1|CF207787
EST:     TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTG                         GATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA
genomic: TTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGTTTGTGgtaatcaaaa ... aatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttcataattttttggcattttgtaaggctaatctcacatacaatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTACCTGTCCTCCTTGTCATTTCTCAGTATGTTTCAATGGAGCTGATGAAGC
                                  atctcac  putative branch site (score: 3)
     tcataatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttaattccaacaccaagacctcatttgaccggcactgaatggataatttcataattttttggcattttgtaaggctaatctcacatacaatcctacagGATGGCCATCCACCATTGGGCTGGCAAGACACTGCAGCATACCTTGTTTTACCTGTCCTCCTTGTCATTTCTCAGTATGTTTCAATGGAGCTGATGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - -acaccaa
- - - - - - - - - -acctcat
- - - - - - - - - - - - - - - - - - -tgaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatac