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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaatttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataatgccatggtgtcc...

Basic information

species Glycine max
transcript GLYMA08G18240.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 5'ss of exon 7
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaatttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataatgccatggtgtcc
 || || ||||||||||||||||| || ||||||||||| || |||||||  ||||||||||||||||  || |||||||||||||| |||||||| || ||| ||      ||    | |    | || ||     || |  |    || ||   |     || |   |  ||| |       ||||||   | |    
CCCTCCAAACATGATTGTTATTCGCTCCTTTGATGTCAACAAGCCTGGTTCAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGCAGCATTCTCAGAgtatgt------gttctctcctgtaacataattaaatattttaatcagtagttttttatgttaagtatgagctgaat-----ggtaatgcttcgttccag

upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 5'ss of exon 7
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaatttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataatgccatggtgtcc
 || || ||||||||||| ||||| || ||||||||||| || |||||||  ||||||||||||||||  || |||||||||||||| ||||| || || ||| ||   ||      | |   || ||    | ||  |   ||||   | ||    | ||  |  |   | | |  ||   | |  | |  |  |    
CCCTCCAAACATGATTGTCATTCGCTCCTTTGATGTCAACAAGCCTGGTTCAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGCAGCATCCTCAGAgtatgt--attccctcgtgtgtcatgtaattagattttttatcact---acttttgggttattaggtatgacttaaattgtga-tgcttcttttatag--

upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G117900_T02 (Zea mays), 5'ss of exon 7
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaatttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataatgccatggtgtcc
 || || ||||||||||||||||| || |||||||| || || |||||||  |||||||| ||||||| ||| |||||||||||||| || || || |||||| ||   |   | | |        || ||| || | ||| || |     |   |||  ||||  |   | || |||| | |                 
GCCTCCCAACATGATTGTTATTCGTTCCTTTGATGTTAACAAGCCTGGTTCAGAGGTTGACGAAATTAGAGGTGGTGTAGCTGGTGGCAGTATCCTCAGGgtatgtatatc--ttagtcatggtgctaccattct-gttctccattatgtttaatatga-acaaaatagcaatggttttgctacag--------------

upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G107654_T01 (Zea mays), 5'ss of exon 7
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttgg--ttggtcaatttccaatatatcatgcttgatctgcactgataattccatgc-tacaatttcaaagtgattttacaaataatgccatggtgtcc
 || || ||||||||||||||||| || |||||||| || || |||||||  ||||| |||||||| |  || |||||||||||||| || ||||| |||||| ||     || ||||             ||    || | | |||||    |    ||   | ||  |||| |  |||||   |                 
ACCTCCCAACATGATTGTTATTCGCTCCTTTGATGTTAACAAGCCTGGTTCAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacatcttagtcatggcatggcgctaca-atctgttttccactgtgtttaatgtgaacaaaacatcaatggtatttttttacag--------------

upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: AT4G18330.2 (Arabidopsis thaliana), 5'ss of exon 6
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaatttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataatgccatggtgtcc
 ||||| || |||||||| ||||| || || ||||||||||||||||| |  | || | ||||||| ||||| ||||| ||||||||||| || ||   |||| |||      |  || ||   | | ||     || |||   ||||   |   |   |  | | | ||  ||  | |     |  |            
ACCACCAAAGATGATTGTGATTCGTTCTTTCGATGTCAATAAACCTGGCTCGGCGGGTCATGAAATGAAAGGTGGTGTTGCTGGTGGAAGTATCCTCCAGgtatgtt------tttatctctc-tgtttctcctctgttcttacctgactgtgaaacaatttagtattaatatgtgtctctctttgtttg----------

upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: AT4G18330.1 (Arabidopsis thaliana), 5'ss of exon 6
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttg--gttggtcaatttccaatatat-catgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataatgccatggtgtcc
 ||||| || |||||||| ||||| || || ||||||||||||||||| |  | || | ||||||| ||||| ||||| ||||||||||| || ||   |||| |||    |   ||  ||||   | | | | | | ||| |||     | ||||   |  ||  || |     |  || |     |  |   |  |     
ACCACCAAAGATGATTGTGATTCGTTCTTTCGATGTCAATAAACCTGGCTCGGCGGGTCATGAAATGAAAGGTGGTGTTGCTGGTGGAAGTATCCTCCAGgtatgtttttatctctctgtttctcctctgttcttacctga-ctgtga-aacaatttagtattaatatgtgtctctctttgtttgggtgttttgaaag-----

upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 5'ss of exon 7
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgta---ggttggttggtcaatttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataatgccatggtgtcc
 || || || ||||| || |||||||| ||||||||||| ||||||||||||||||||||||| || ||||| || || || |||||||| || ||  |||||     |   |   ||    |      | |  ||| |  |  | ||    |  |  ||         |||   |   || || |    |    ||  |   
ACCCCCAAATATGATAGTGATTCGGTCTTTTGATGTCAACAAACCTGGTTATGAGGTTGATGAGATCAAAGGTGGAGTTGCAGGTGGAAGTATCCTACGGgtatctattctctctctctccctttctcttgttgtgcctcttaagtacatcaagctttatatggtgtaatcagtatctcttaactacatgtatattgtag---

upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: AT2G18720.1 (Arabidopsis thaliana), 5'ss of exon 5
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaat-ttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataatgccatggtgtcc
 || || |  |||||||| ||||| || |||||||||||||||||||| | |||   |||||  || ||||| || || || ||||| || || ||   ||||       |  |||||   || | | |  | | |  |||    | | | | || |||    || ||     |   ||| |      |||          
ACCTCCAAGAATGATTGTGATTCGTTCTTTTGATGTCAATAAACCTGGCTCTGATTATGATGGTATGAAAGGTGGAGTTGCAGGTGGGAGTATCCTTCAGgtaaaaca--tactcaataccccgaaaaactaggataaatc---gcggttgaatcaatgt---aacttatgtctctctttgctttgtttgcag--------

upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 5'ss of exon 6
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaatttccaatatatc---atgcttgatctgcactgataattcc-----atgctacaatttcaaagtgattttacaaataatgccatggtgtcc
 ||||| || |||||||| ||||||||||||||||||||||| ||||| | |||||||||||| || | ||| ||||| ||||||||||||||||| |||||| ||   |     | |     | | ||    | |   || ||      ||  |||      ||||| |   | |||| || |||  |   |  | |||        
ACCACCAAATATGATTGTGATTCGGTCATTTGATGTCAATAAGCCTGGGTTTGAGGTTGATGAGATAAGAGGTGGTGTTGCTGGTGGAAGCATTCTCAGGgtatgtatctcctctattacttcagagattcagaagtaagaactatgtaaatgcttcacatggatgctgctgatgcaaaatgctttatc---tgcttccacat-----

upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 5'ss of exon 7
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaatttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataatgccatg-gtgtcc----
 ||||| || ||||||||||||||||||||||||||||| || ||||| | |||||||||||| || | ||| ||||| ||||||||||||||||| |||||| |||  |      ||||   || |   | | ||| |    |    ||  |  | ||| ||  || |   || |  | ||||       ||  |  |||    
ACCACCAAATATGATTGTTATTCGGTCATTTGATGTCAACAAGCCTGGGTTTGAGGTTGATGAGATAAGAGGTGGTGTTGCTGGTGGAAGCATTCTCAGGgtatgtttctc-----atttattatttcagaggtttggtagtaagaactatgtaaaggcttcacattgatgctgttggtgcaaaatgcttgatctgcttccacat

upper sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
lower sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 6
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaatttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataat---gccatggtgtcc
||| || |||||||| ||||||||||| || |||||||| || ||||||   || ||||| ||||| || || || || |||||||| || |||||||||||| |||| |  ||||| |   |  || | ||     |     ||  ||  |     | |    |    |  ||  |  |    |||      || |  ||||
TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt--gtcaagtgtgataatgtaatcggccaatcagacatatg-tgttgggttcatgtccggacatggctgcagggttaagttgatcaggtagtcc

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|254316161|gb|GR825970.1|GR825970
EST:     ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGG                         GGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGTT
genomic: ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggt ... ctctttgcagGGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGTT
EST: gi|192321216|gb|FK014306.1|FK014306
EST:     ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGG                         GGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGTT
genomic: ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggt ... ctctttgcagGGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGTT
EST: gi|9259268|gb|BE347476.1|BE347476
EST:     ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGG                         GGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGTT
genomic: ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggt ... ctctttgcagGGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGTT
EST: gi|193451925|gb|FK418975.1|FK418975
EST:     ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGG                         GGTTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGT
genomic: ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggt ... ctctttgcagGGT-GTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGT
EST: gi|207752019|gb|GD722136.1|GD722136
EST:     ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGG                         GGTNTTTTGAAGGT
genomic: ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggt ... ctctttgcagGGTGTTTTGAAGGT
EST: gi|105632214|gb|DW246363.1|DW246363
EST:     ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGG                         GGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGTT
genomic: ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggt ... ctctttgcagGGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGTT
EST: gi|208285532|gb|GE082468.1|GE082468
EST:     GGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGG                         GGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCAGGCATTGTTGTT
genomic: GGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggt ... ctctttgcagGGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGTT
EST: gi|18692825|gb|BM521673.1|BM521673
EST:     ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGG                         GGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCCG-CCTGGCATT
genomic: ATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggt ... ctctttgcagGGTGTTTTGAAGGTCAATCAATTCATTGAAGTTC-GTCCTGGCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaatttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataatgccatggtgtcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG