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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA

Basic information

species Glycine max
transcript GLYMA07G03890.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 15
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
                                      |||| ||||   ||  |||   | ||  || |||  |||||  | ||| ||||  |||     |||||  || |||||||          |||  |   ||||   ||||||     |  |||| || || |||| ||| ||||| || ||||||||||||||||||||||| || |  |||||    || ||| | || ||||| ||||||||
--------------------------------------gtatatattg--tgtgctccatgcaagaatttttattttgt--taatgtattttctattgtagtattttgtgcactacaa----------atttatcccgttg---tacatt-----tacagGTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAA

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
                                           ||  ||| |    ||||  || ||| | |||| | |       ||||   ||||||   | ||  ||     || |  |   |    |    | |||  |   | ||||   |  |||| |||||||||| ||||||||| || ||||||||||||||||||||| |||| | |||||||   || ||| | || ||||| || || ||
------------------------------------------gtaaatatagtctgctcgaaaa-catttcttctgttt------aaattctctatatgggcacttcatgt----catgacttcaattgcttacatagttataa-gctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G095348_T03 (Zea mays), 3'ss of exon 15
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
                                         |  |  || |  ||||   | || | | || |     |||   | | ||   ||||||   | ||  |||   || |   |   |   ||      |||  |   | || |   |  |||| |||||||||| ||||||||| || ||||||||| | |||||||||||||| | |||||||   || ||| | || ||||| || || ||
----------------------------------------gtaaaaatagtctactccttgaaaacgttttct-----tctgtttaagttctctatatggccactttgtgagtcacgac--ttcaattgtttacacagttataa-gctttgtacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACCTATTGGGATATCTTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTTAA

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 16
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattc------ctgttgttgcattacattatggatt-tagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
                                                         |    | | |  ||  |  |    |   ||||  |||  ||| |||| | ||  | | |   ||   |    ||       || |   |  |  |  | |||  ||  ||||||||||||||||||| ||||| || |||||||| || || ||||||||||| | |||||||   || ||| | || ||||| ||||| ||
--------------------------------------------------------gttaacacttaatttcaccataatctgtagaat--cttgaatgcatatctgtttgattcctgagagtgtttggttttatgtgctatctatttaccatctcatgtgttacagGTTACTACAATGTTTCACTTGGATCGGCCTATGTATTTATTAGGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAA

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 19
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatt--tcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
                                                            ||||   || |||||  || ||    ||      || ||||| | ||||||    |  ||     || || | |   |       ||| ||||       |||| |||||||||| |||| ||||||||||||||||||||||||| ||||| || |  ||||| | ||| |||||||| |||||||| |||||
------------------------------------------------------------gtaaggctcatttctaggtttttggaaagaaacgttttatgttt-tttattttgttgtaattgagattcagtactcctc------ttatatta------cagGTAACTACAATGTATCATCTGGACCGTCCTATGTACTTGTTGGGTTATCTCGCTAATCAAAGCAGGGTTTATTTGATTGACAAAGAGTTCAA

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaattt-cttatatgtatatttat-tgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
                                                                             ||  ||| || | |  || ||| | || | || |  |  |     || ||| |||  ||| |  |  |      | |||    |||| || ||||||| |||||||||||| || ||||| ||||| || ||| |||||| ||||||   ||| || ||| ||||||||||||||||
-----------------------------------------------------------------------------gtactcaagagtctatttttatttctaatcatctttatgagctacattatataatagctgctaatatacc----tgtgg---cagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
                                                                  ||  |   | | | ||  | | | |  | |     |  |||| |||||    ||||  ||  ||    |||| |     ||||  |     ||||| || ||||||| |||||||||||| || ||||| ||||||||||||||||| || ||||||  ||| |  ||| ||||||||||||||||
----------------------------------------------------------------gtattgtgcatatatgttggttactctgatttggaagttgttat-gaact----ggattcta--atgatggttgcta----acatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 15
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttct-tatatgtatatttattgaactacaaggatcataca-attcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
                                                       | | |   ||  ||    |||    |  | | |||||  ||| || | ||    |  | | || ||||       |    | |||||  || ||  ||||  |  |||| || |||||||||||||||||||| |||||||| |||||||||||||| || |  |||||   ||| ||| | ||||||||||| |||||
------------------------------------------------------gtattgtgtattgtccacccttgtcttgaaagtatttccatatgtgcagatgatatccatttcatggatttcttggagcttttttgttaaataaccatatgt-tccagGTAACCACAATGTTTCATTTGGACCGGCCTATGTATTTGTTGGGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAA

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 15
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
                                                                  ||       |||  | || |   |  || ||| |||||    |  | |  ||||  ||    ||     |||||     |  | |||  || |||| || || |||||||| |||||||| |||||||| ||||| |||||||||||||| ||||||   || ||| | ||||||||||| || ||
----------------------------------------------------------------gtataagagagttgattccaggttgtatttctatatatatgatcttcattctaaggtgca-gtcatataaattgtta----atgtgatgatttcagGTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAA

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|254341657|gb|GR852794.1|GR852794
EST:     TTATCTACAGCAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAG                         GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTT
genomic: TTATCTACAGCAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttatac ... atggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTT
EST: gi|120532392|gb|EH260525.1|EH260525
EST:     TTATCTACAACAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAG                         GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTT
genomic: TTATCTACAGCAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttatac ... atggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
                                     attacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA