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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaaagcaggcaacaaaaaaaccttacagttaagggataaatacattattcatggttgaattttttccatgtgcagGCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGTGGTGATGCCAAGGGTATGGCCAAAGATGTTCATCGAACTTTGCATACCA

Basic information

species Vitis vinifera
transcript Vv18s0001g07630.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07630.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA06G10180.2 (Glycine max), 3'ss of exon 16
gtgagtaaaagcaggcaacaaaaaaaccttacagttaag-ggataaatacattattcatggttgaattttttccatgtgcagGCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGTGGTGATGCCAAGGGTATGGCCAAAGATGTTCATCGAACTTTGCATACCA
|| |||  ||  ||    | |       | | |  ||   |||||| |   || | | ||  | ||||||||  ||||||||||  || |  | |||| | | || ||||| || || |||||||| || ||||||||||||||||||||||||| |||||||||||||||| | |||||||
gtaagtgcaaatagcagcctagtggggatcaaatgtagccggataagt---ttttccctgcattaattttttt-atgtgcagGCTGCACAGCTGTGGAGTTTGATTTCTCAAGGAGGTTATCTTTACGTCTGTGGTGATGCCAAGGGTATGGCCAGAGATGTTCATCGAACTCTTCATACCA

upper sequence: Vv18s0001g07630.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA14G36070.1 (Glycine max), 3'ss of exon 16
gtgagtaaaagcaggcaacaaaaaaaccttacagttaagggataaatacattattcatggttgaattttttccatgtgcagGCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGTGGTGATGCCAAGGGTATGGCCAAAGATGTTCATCGAACTTTGCATACCA
|| |||   |  |   | | |  |  |   |||| |     ||  ||| ||| ||  || ||| |||  |||  |||||||||  || |  | |||||| | || |||||||| || ||||||||||||||||||||||| ||||| ||||||  |||||||||||| ||| | |||||||
gtaagtgtcattatcaacctagtaggca--acagatgcactatggataaattttt--tgattgcattaattctgtgtgcagGCTGCAAATCTGTGGAATTTGATTTCTCAGGGAGGTTATCTTTATGTTTGTGGTGATGCTAAGGGCATGGCCCGAGATGTTCATCGGACTCTTCATACCA

upper sequence: Vv18s0001g07630.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA04G10200.1 (Glycine max), 3'ss of exon 16
gtgagtaaaagcaggcaacaaaaaaaccttacagttaag-ggataaatacattattcatggttgaattttttccatgtgcagGCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGTGGTGATGCCAAGGGTATGGCCAAAGATGTTCATCGAACTTTGCATACCA
|| |||   |  ||    | |  |    | | |  |||  ||||||||  |||        || | ||||||  ||||||||||  || |  | |||| | | || ||||| || || |||||||| || ||||||||||||||||||||||||| |||||||||||||| | | |||||||
gtaagtgcgaatagcagcctagtagggatcaaatgtaaccggataaat-tatttcctgca-ttaatttttttttatgtgcagGCTGCACATCTGTGGAGTTTGATTTCTCAAGGAGGTTATCTTTACGTCTGTGGTGATGCCAAGGGTATGGCCAGAGATGTTCATCGAATTCTTCATACCA

upper sequence: Vv18s0001g07630.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA02G37850.1 (Glycine max), 3'ss of exon 16
gtgagtaaaagcaggcaacaaaaaaacc--ttacagttaagggataaatacattattcatggttgaattttttccatgtgcagGCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGTGGTGATGCCAAGGGTATGGCCAAAGATGTTCATCGAACTTTGCATACCA-
    ||||  |     | |||   |       |||| |     ||  ||| ||| ||  || ||| |||  |||  |||||||||| || |  | |||||| | || ||||||||||| |||||||||||||||| |||| | ||||| ||||||| |||||||||||| ||| | | ||||| 
----gtaagcgtcattatcaacctagttggcaacagatgcactatggataaattttt--tgattgcattagttctgtgtgcagGCAGCAAATCTGTGGAATTTGATTTCTCAGGGGGGTTATCTTTATGTTTGTG-TGATCCTAAGGGCATGGCCAGAGATGTTCATCGGACTCTTCTTACCAT

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|30125241|gb|CB910580.1|CB910580
EST:     CACGAGAGGGGCCACAAAAGGAGTATGTGCAACATAAGATGATGGATAGA                         GCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGT
genomic: CACGAGAGGGGCCACAAAAGGAGTATGTGCAACATAAGATGATGGATAGAgtgagtaaaa ... ccatgtgcagGCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGT
EST: gi|27584661|gb|CB007356.1|CB007356
EST:     CACGAGAGGGGCCACAAAAGGAGTATGTGCAACATAAGATGATGGATAGA                         GCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGT
genomic: CACGAGAGGGGCCACAAAAGGAGTATGTGCAACATAAGATGATGGATAGAgtgagtaaaa ... ccatgtgcagGCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGT
EST: gi|30125286|gb|CB910625.1|CB910625
EST:     CACGAGAGGGGCCACAAAAGGAGTATGTGCAACATAAGATGATGGATAGA                         GCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGT
genomic: CACGAGAGGGGCCACAAAAGGAGTATGTGCAACATAAGATGATGGATAGAgtgagtaaaa ... ccatgtgcagGCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttacagttaagggataaatacattattcatggttgaattttttccatgtgcagGCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGTGGTGATGCCAAGGGTATGGCCAAAGATGTTCATCGAACTTTGCATACCA
 accttac  putative branch site (score: 3)
                                       ttttttccat  putative PPT
               ataaatacattattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaaaagcaggcaacaaaaaaaccttacagttaagggataaatacattattcatggttgaattttttccatgtgcagGCATCATACATATGGAATATAATCTCTCAGGGGGGATATCTTTATGTTTGTGGTGATGCCAAGGGTATGGCCAAAGATGTTCATCGAACTTTGCATACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG