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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtatagcagagtcctatatgcattacttaaaaaaactaattaaacatgcaatatatctttagtctgctactcacaacgatttacttgccttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATGGAGAGTGGTTTCCTGCTCAGTGACCCCAAGCATTTTGCCTCTAATATCT

Basic information

species Vitis vinifera
transcript Vv18s0001g14500.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 14
-tgtatagcagagtcctatatgcattacttaaaaaaactaattaaacatgcaatatatctttagtctgctactcacaacgatttacttgccttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATGGAGAGTGGTTTCCTGCTCAGTGACCCCAAGCATTTTGCCTCTAATATCT
 |  ||   ||| |  || |  ||||   | |   | ||  ||   ||    | ||    ||  |||| ||      || || | |||  |||   ||||||||||||| || ||| | ||||||||||| |||||||| || |||||| | || || || ||||||||   ||| |||||| ||||||| ||    || |
gtacattctagattattaga-acattttctgaggcatctctttcctcaactcaaatggggtttatctgttaac----acaatctgctttactt---ttcagGATGAGGGTGTGAAGCATACAGCACAGCTGATGTACCAGACTGCACTCTTTGAAAGCGGCTTCCTGCTTGATGATCCCAAGGATTTTGCTTCCCGGATTT

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 14
tgtatagcagagtcctatatgcattactta-aaaaaactaattaaacatgcaatatatctttagtctgctactcacaacgatttacttgcc--ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATGGAGAGTGGTTTCCTGCTCAGTGACCCCAAGCATTTTGCCTCTAATATCT
                    | |  ||  | | || ||  || ||   |    | ||  |   ||||  ||   | |   | | || | ||   | |  |||||||||| | || ||| |||||||||||||||||||||| |||||  | || |||||||| ||| | ||||  ||||| ||  | |||||  |   ||| |
--------------------gtaaaacaaacataagacccatcaattcttttttttacttactgtctattagagaaataaactaacataccaaattctctcagGATGAGAGTGTGAAGGAAACAGCACAGCTCATGTACCAGACAGCTTTGATCGAGAGTGGATTCATACTCACCGACCCAAAAGACTTTGCTGCCCGTATTT
















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|110421948|gb|EC988254.1|EC988254
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|110689117|gb|EE065061.1|EE065061
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|110399268|gb|EC965766.1|EC965766
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|33401642|gb|CF207269.1|CF207269
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|33410380|gb|CF216007.1|CF216007
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|30297638|gb|CB974432.1|CB974432
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|28970695|gb|CB349728.1|CB349728
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|33401721|gb|CF207348.1|CF207348
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|22009174|gb|BQ794208.1|BQ794208
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|33410302|gb|CF215929.1|CF215929
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|110415390|gb|EC981295.1|EC981295
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|83275613|gb|DV939621.1|DV939621
EST:     CAAGGAG-TTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: CAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|110719823|gb|EE095290.1|EE095290
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTANTAAAGGACAGTGAG                         GATGAAGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|294966850|gb|GW839725.1|GW839725
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
EST: gi|110419250|gb|EC985463.1|EC985463
EST:     GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAG                         GATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG
genomic: GGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgtttta ... ttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcaatatatctttagtctgctactcacaacgatttacttgccttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATGGAGAGTGGTTTCCTGCTCAGTGACCCCAAGCATTTTGCCTCTAATATCT
                       tactcac  putative branch site (score: 1)
                                   tttacttgccttccct  putative PPT
     aatatatctttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtatagcagagtcctatatgcattacttaaaaaaactaattaaacatgcaatatatctttagtctgctactcacaacgatttacttgccttcccttcagGATGAGGGCGTAAAGAAAACAGCACAGCTCATGTACCAAACAGCACTCATGGAGAGTGGTTTCCTGCTCAGTGACCCCAAGCATTTTGCCTCTAATATCT

- - - - - - - - -tatgcat
- - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttgcc