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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgtaggccctttacatgtaattcatacttcaaatttatactggtagctagctaaagattgtcatttcatgcccccacctcctcccaaacacatacacgcttcaagactgagtgcttttgtgtgtgtgaaagtttgtgagcaatgataataatctaacaccatgctttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGTCCTGGTCATTAACAAAATTGCCCCACAAAATTGGAAG

Basic information

species Glycine max
transcript GLYMA20G02940.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02940.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g00170.t01 (Vitis vinifera), 3'ss of exon 4
gtaaatgtaggccctttacatgtaattcatacttcaaatttatactggtagctagctaaagattgtcatttcatgcccccacctcctcccaaacacatacacgcttcaagactgagtgcttttgtgtgtgtgaaagtttgtgagcaatgataataatcta-acaccatgctttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGTCCTGGTCATTAACAAAATTGCCCCACAAAATTGGAAG
                                                                                || ||     | | |  ||     ||      || |||| | |||||||| || ||     |  ||| || |   | ||       |||| || | ||||| ||||| | |||||| |||||||||||   |||||  ||| |||||||||| || || ||| ||||| ||||||||| ||||||||||
----------------------------------------------------------------------------gtaaacttctaattatataagtaattaattttcacttgtgtgcatctgtgtgtgagagag-----ggacaaggagagctaactgtgttttatgcctt-tttgcagTTTCACGAGGAAACTTTTGGTTGCAGTTGTGGATAAGTGGAACAGTCATGTGCTTGTTATTGACAAAGTTGCCCCACCAAATTGGAAG
















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|208255999|gb|GE055638.1|GE055638
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
EST: gi|192314699|gb|FK006625.1|FK006625
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
EST: gi|9898905|gb|BE607873.1|BE607873
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
EST: gi|58019927|gb|CX706669.1|CX706669
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
EST: gi|192314700|gb|FK006626.1|FK006626
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
EST: gi|209727508|gb|BW663744.1|BW663744
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
EST: gi|51336196|gb|CO980062.1|CO980062
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
EST: gi|9258967|gb|BE347114.1|BE347114
EST:     AAGTCCTTACAGCTCCTACAAAGCTGGTATACAACAGACTGGATTT-AAG                         ATTCACCAAGAAACTATTGGTTGCCGTCANGGATACATGGGACAGTCATG
genomic: AAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTG-ATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATG
EST: gi|57574769|gb|CX547744.1|CX547744
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
EST: gi|192294862|gb|FG987551.1|FG987551
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCA
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCA
EST: gi|192316707|gb|FK006410.1|FK006410
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATATAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
EST: gi|9899175|gb|BE608202.1|BE608202
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
EST: gi|26058037|gb|CA800951.1|CA800951
EST:     GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG                         ATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT
genomic: GAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAGgtaaatgtag ... ttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgtgaaagtttgtgagcaatgataataatctaacaccatgctttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGTCCTGGTCATTAACAAAATTGCCCCACAAAATTGGAAG
                              atctaac  putative branch site (score: 2)
                                           ctttatct  putative PPT
                    aatgataataatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgtaggccctttacatgtaattcatacttcaaatttatactggtagctagctaaagattgtcatttcatgcccccacctcctcccaaacacatacacgcttcaagactgagtgcttttgtgtgtgtgaaagtttgtgagcaatgataataatctaacaccatgctttatctgcagATTCACCAAGAAACTATTGGTTGCAGTCAGGGATACATGGGACAGTCATGTCCTGGTCATTAACAAAATTGCCCCACAAAATTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG