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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaaataaggaaacaactgagacaattagatttcatattggatgtaagggtgccttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT

Basic information

species Glycine max
transcript GLYMA07G01260.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
gtaaggaaataaggaaacaactgagacaattagatttcatattggatgtaa--gggtgccttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
             |    || ||   |  |||  |||| ||   ||| |    || | | || |     | | ||    |  |||         ||    |  | ||||   ||  ||||| ||||| ||||||||  | || || || || || |||||||||||||| || ||||| |||||||| ||||| |||||||| ||||| |  ||
-------------gtgcgaaatgttgc--ttatgtttcttaaccgattttcttggatacattctggacttcttttgtggtaatctactaacatttttccgtgtgttattaa-agCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT

upper sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 3
gtaaggaaataaggaaacaactgagacaattagatttcatattggatgtaagggt---gccttttctgactatgttacctttg---tcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
                      | || || | | || |  | ||  | |     |    | | || ||   |    | ||      |||   |    |    |||    |  ||  ||  ||||| ||||| |||||||| || || || ||||| || |||||||||||||| || ||||| ||||| || || || |||||||||||||| | |||
----------------------gtgagaacttgtttccccaatgcttttccttctcaaccatcttttgggaactccagctaaaaattctgaacacttacaattttgttgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT

upper sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaggaaataaggaaacaactgagacaattagatttcatattggatgtaagggtgccttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
         ||| |     | |    |   | || ||| | ||   | |    || | | ||      | |||      | ||        |||    ||  || ||  ||| || ||| || || ||||| || || ||| | ||||| ||||||||||| ||||| || ||||| ||||||||  ||||||||||| |||| || |  ||
--------gtaatgct-tgatttctgctcctggagttcttttt---ttttttcgttcttgtttgatggaagttgtaaaaggct--gtactgattgaaataaaat-ttcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGGCTGTGCAGATACAGCAAGAGGCATCTAAATTTGGTTCATCCTCAAAAAT

upper sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtaaggaaataaggaaacaactgagacaattagatttcatattggatgtaagggtgccttttctgac-tatgttacctttgtcttgccgtccattcgtttacgatattttc--agATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
                       | | |     |       | |   |    |  || |     |  || ||    |   | | |  ||  || ||    | ||       |    || ||  |  |||||||  || ||| |||||||| |||||||| |||||||| ||||||||||||||||||||||| || ||||||||||| ||  ||||||||||||||||||| |||||
gtataagtgtctttctaattcgttgatgtcgctaatttctgatttctatctatctatctatctatctatatatatatatatatgcacacacatttttttctagttacaagttttggtctttctctgtattttctcagCTCCAGGAGATGGCCCAATTGTATTAGTTTTAGCTCCAACTCGTGAACTTGCTGTTCAGATACAACAAGAAGCAGCTAAATTTGGTGCATCATCGAGGAT

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|193441190|gb|FK409983.1|FK409983
EST:     TGCTTACTTGTTGCCATCCATTGTGCATGTTAATGCTCAGCCTATTCTAA                         ATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTG
genomic: TGCTTACTTGTTGCCATCCATTGTGCATGTTAATGCTCAGCCTATTCTAAgtaaggaaat ... atattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTG
EST: gi|193512144|gb|FK467704.1|FK467704
EST:     ATTGTGCATGTTAATGCCCAGCCTATTCTAA                         ATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTG
genomic: ATTGTGCATGTTAATGCTCAGCCTATTCTAAgtaaggaaat ... atattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTG
EST: gi|207764082|gb|GD738905.1|GD738905
EST:     CCATCCATTGTGCATGTTAATGCTCAGCCTATTCTAA                         ATCCTGGAGATGGACCAATTGTGTTAGTTTTTGGCTCCAACTCGTGAACTT
genomic: CCATCCATTGTGCATGTTAATGCTCAGCCTATTCTAAgtaaggaaat ... atattttcagATCCTGGAGATGGACCAATTGTGTTAG-TTTTGGCTCCAACTCGTGAACTT
EST: gi|209699629|gb|BW655721.1|BW655721
EST:     TGCTTACTTGTTGCCATCCATTGTGCATGTTAATGCTCAGCCTATTCTAA                         ATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTG
genomic: TGCTTACTTGTTGCCATCCATTGTGCATGTTAATGCTCAGCCTATTCTAAgtaaggaaat ... atattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTG
EST: gi|10709520|gb|BF009244.1|BF009244
EST:     GCTTACTTTGT-GCCATCCATTGTGCATGTTAATGCTCAGCCTATTCTAA                         ATCCTGGAGATGGACCAATTGTG
genomic: GCTTACTT-GTTGCCATCCATTGTGCATGTTAATGCTCAGCCTATTCTAAgtaaggaaat ... atattttcagATCCTGGAGATGGACCAATTGTG
EST: gi|209720525|gb|BW675024.1|BW675024
EST:     TGCTTACTTGTTGCCATCCATTGTGCATGTTAATGCTCAGCCTATTCTAA                         ATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCNTC-AACTCGTGAACTT
genomic: TGCTTACTTGTTGCCATCCATTGTGCATGTTAATGCTCAGCCTATTCTAAgtaaggaaat ... atattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGC-TCCAACTCGTGAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
   ttctgac  putative branch site (score: 2)
                                              tattttc  putative PPT
                                             atattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaaataaggaaacaactgagacaattagatttcatattggatgtaagggtgccttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG