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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaataaacaaaagtttatagtgactaaaatcatcaaactgatgtattatagagacctttaagcataaaatgtgtgatcaaaattgcaaatggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGAGACCCAAGTGAATCCTGCTGTGTGGGAAATTAGTGGGCACATGGTGCTG

Basic information

species Glycine max
transcript GLYMA18G10430.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G10430.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0090g01000.t01 (Vitis vinifera), 3'ss of exon 6
aaaataaacaaaagtttatagtg-actaaaatcatcaaactgatgtattatagagacctttaagcataaaatgtg-tgatcaaaattgcaaat-ggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGAGACCCAAGTGAATCCTGCTGTGTGGGAAATTAGTGGGCACATGGTGCTG-
  || |    | |   ||   |  |||   ||   |||  |  ||    ||   |   | |||   || | |    | |||    || |  || |  ||||||||| ||||| ||||||||||| ||||| ||||||| ||  ||||||||||| ||||||||||| || ||||| |||||  ||||||| || || |||||| 
gtaaaatttcagatcgtaggctacactggtatggccaactt--tgctgcatttgggtttctaattttagatttaactcatctccttttcttattgaataaacagTGTTATGCTGAGAAACAAGCTCTTGGGGAAGTGAATCAGGAGCTTCTGGACACCCAAGTGAACCCAGCTGTCTGGGAGGTTAGTGGACATATTGTGCTGA

upper sequence: GLYMA18G10430.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ25760 (Selaginella moellendorffii), 3'ss of exon 6
aaaataaacaaaagtttatagtgactaaaatcatcaaactgatgtattatagagacctttaagcataaaatgtgtgatcaaaattgcaaatggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGAGACCCAAGTGAATCCTGCTGTGTGGGAAATTAGTGGGCACATGGTGCTG-
                                 | | | | |  ||||||||     ||| | ||||  || | | || |  |||        ||   ||||| ||||| ||||||||||| | ||| || ||   || |||| || | || || |||||||||||||| ||||||||||| ||||| ||||| ||  || 
--------------------------------gtaagatttagatattatag-----ttttatcatatcatat-taattattattt-------ttgttcagTGTTATGCTGAGAAACAAGCTCGTGGTGAGGTTGATCTTGAGATTTTAGAAACTCAAGTGAATCCTGCAGTGTGGGAAATAAGTGGTCACATTGTTTTGA

upper sequence: GLYMA18G10430.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ22189 (Selaginella moellendorffii), 3'ss of exon 6
aaaataaacaaaagtttatagtgactaaaatcatcaaactgatgtattatagagacctttaagcataaaatgtgtgatcaaaattgcaaatggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGAGACCCAAGTGAATCCTGCTGTGTGGGAAATTAGTGGGCACATGGTGCTG-
                                 | | | | |  ||||||||     ||| | ||||  || | | || |  |||        ||   ||||| ||||| ||||||||||| | ||| |||||   || |||| || | || || |||||||||||||| ||||||||||| ||||| ||||| ||  || 
--------------------------------gtaagatttagatattatag-----ttttatcatatcatat-taattattattt-------ttgttcagTGTTATGCTGAGAAACAAGCTCGTGGTGAAGTTGATCTTGAGATTTTAGAAACTCAAGTGAATCCTGCAGTGTGGGAAATAAGTGGTCACATTGTTTTGA

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|8286331|gb|BE023890.1|BE023890
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|16345579|gb|BI971174.1|BI971174
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|8283980|gb|BE021539.1|BE021539
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|9819840|gb|BE555416.1|BE555416
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|192311633|gb|FK003550.1|FK003550
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|120495753|gb|EH223920.1|EH223920
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|192315959|gb|FK007092.1|FK007092
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|120496039|gb|EH224206.1|EH224206
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|192311632|gb|FK003549.1|FK003549
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|21888834|gb|BQ742047.1|BQ742047
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|192315960|gb|FK007093.1|FK007093
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACA                         GTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
EST: gi|192317486|gb|FK011276.1|FK011276
EST:     TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACG                         GTACTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA
genomic: TACAATGTACTTATTTCAGATTGTGGAAGGCAAATATTTCTCTTACCACAggtaaatttg ... tggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatagagacctttaagcataaaatgtgtgatcaaaattgcaaatggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGAGACCCAAGTGAATCCTGCTGTGTGGGAAATTAGTGGGCACATGGTGCTG
            tttaagcataaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaataaacaaaagtttatagtgactaaaatcatcaaactgatgtattatagagacctttaagcataaaatgtgtgatcaaaattgcaaatggttaaacaGTGCTATGCAGAGAAACAAGCCCTTGGAGAAGTGAGTCCTGAGCTTCTGGAGACCCAAGTGAATCCTGCTGTGTGGGAAATTAGTGGGCACATGGTGCTG

aaaataa
- - - - - - - - - - gtgacta
- - - - - - - - - - - - - - - - - - -actgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtga