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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatgaaaagcttatctccctattgcccacatgtgattcttaagtcatgtaactgatttgccctgtatgttctggttctgcaagctcagtgcaaaa...

Basic information

species Glycine max
transcript GLYMA01G09400.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G09400.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G137541_T01 (Zea mays), 5'ss of exon 4
GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatgaaaagcttatctccctattgcccacatgtgattcttaagtcatgtaactgatttgccctgtatgttctggttctgcaag---ctcagtgcaaaa--------------------------------------------------------------------------------------------
|||||||||||||| || ||||| || || ||||||||||| || ||||| || ||| |||| |||||||||   || | || | |  | ||| | |    ||   |||  | | | ||| ||     ||||||  |  | |   | |  | || ||   || ||  |   |                                                                                            
GTCACTGGCAAGGCGGTGATGCTTGACGAGATCATCAACTACGTTCAGTCCCTGCAAAGACAAGTTGAGgta---ataacaaacat-cccccccaatatatac---tgagacctgaatcaagttgtc-atttgcaatagaggaagtagaacagctagacactgagaccctgaatatgaacacagttcctctttctacaaaaccctcgttacatacatacataccgatggcaggcacatcaaaacactgaacgaatctcttgcag

upper sequence: GLYMA01G09400.1 (Glycine max), 5'ss of exon 5
lower sequence: AT1G68920.2 (Arabidopsis thaliana), 5'ss of exon 5
GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatgaaaagcttatctccctattgcccacatgtgattcttaagtcatgtaactgatttgccctgtatgttctggttctgcaagctcagtgcaaaa
|| ||||| |||||||| ||||| || |||||||| ||||| ||||| ||||| ||||| || |||||||||||         | ||  || | |       |   |  |  ||   || |||||   |||     ||    ||    || |||     |||       
GTGACTGGGAAGGCAGTTATGCTTGACGAAATCATAAACTACGTACAATCACTACAACGCCAAGTTGAGgtatgc---cgtttcctaattctcaacgaggtgctctttgtgtttgcttcttgtaatcaattc-ttttgctcatttctcttttgcttaaacag-------

upper sequence: GLYMA01G09400.1 (Glycine max), 5'ss of exon 5
lower sequence: AT1G26260.2 (Arabidopsis thaliana), 5'ss of exon 5
GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggat-------------gaaaagcttatctccctattgcccacatgtgattcttaagtcatgtaactgatttgccctgtatgttctggttctgcaagctcagtgcaaaa
|| ||||| |||||||| ||||| ||||||||||| |||||||| || ||||||||| | ||  | ||||| |   |             |||   | ||| | | || || |      |||  ||| | | |  || |    |  |  ||| |    |  |||| | |   || | ||   
GTGACTGGTAAGGCAGTTATGCTCGATGAAATCATTAACTATGTGCAATCACTTCAATGCCAAATCGAGgtttccctttgtttgctttgggaatttcctattttcttagtgtctgttcttgagacttcatttaattagcaacctcactttgtgttagttacttcttcca-tgcatttcag--

upper sequence: GLYMA01G09400.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv01s0010g00740.t01 (Vitis vinifera), 5'ss of exon 5
GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatgg-atgaaaagcttat-ctccctattgcccacatgt-gattcttaagtcatgtaactgatttgccctgtatgttctggttctgcaagctcagtgcaaaa-
|||||||||||||| || ||||||||||||||||| |||||||| || ||||||||||| ||||||||||||||| || ||     |||  || || || ||  | | | | |||| || | || |   | |||||  ||     | |||  |||  ||  ||   | || | 
GTCACTGGCAAGGCGGTCATGCTAGATGAAATCATTAACTATGTGCAATCACTTCAACGGCAGGTTGAGgtatggtattaaggatctatgttctctttttcctccctattggttctcaattgatctggtttatttgttct----atcctgcatcttaaatgtctccgaaacat

upper sequence: GLYMA01G09400.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S68_190V6.1 (Physcomitrella patens), 5'ss of exon 3
-------------------------------GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatgaaaagc-ttatctccctattgcccac---atgtgattcttaagtcatgtaactgatttgccctgtatgttctggttctgcaagctcagtgcaaaa--------------------------------
                               ||||| ||||||||||| ||||| || || |||||||||||||| || || || |||||||| ||||| |||||  |   |  | || ||  |  | |||  |    ||   |||| |   | | | | |    |||   |   |  |   |   || | |   |||    |                                 
CCTGCAGGACCTCGTACCCGGCTGCCGCAAAGTCACCGGCAAGGCAGTCATGCTTGACGAGATCATCAACTATGTTCAATCCCTCCAACGACAAGTTGAAgtatgtctcttacccattttcaacgcactgctaatgctattccattcatgtcttaggcacccttcttgttatcgctagtgatgaattgta-gtctagtattgagttgtatcgtacactttgttatcttttttacag

upper sequence: GLYMA01G09400.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S69_95V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------------GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatgaaaagcttatctccctattgcccacatgtgattcttaagtcatgtaactgatttgccctgtatgttctggttctgcaagctcagtgcaaaa-----------------
                               ||||||||||| ||||| ||||| |||||||||||||| || || ||||| || ||||| || || ||||||   ||       |   | || |  |   ||||  |||   |   |  | | | ||| | |      |||   | |||| || | | | | | | | |                 
CTTGCAGGACCTTGTTCCTGGCTGCCGCAAAGTCACTGGCAAAGCAGTCATGCTCGATGAAATCATCAATTACGTCCAGTCCCTCCAACGTCAAGTCGAGgtac--atccctcattctccgccgttctatacacaattgaaggtggtgatagggatctgctgtaattcatat---caggttatg-atgttaacttccacattttttttgtgttgcag

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|193362293|gb|FK324809.1|FK324809
EST:     TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCTACAGTAAATCCACGG
genomic: TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAATCCACGG
EST: gi|208160240|gb|GD953496.1|GD953496
EST:     TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATA
genomic: TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATA
EST: gi|193467285|gb|FK433924.1|FK433924
EST:     TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCTACAGTAAATCCACGGCTGGATTTTAATATT
genomic: TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
EST: gi|208231305|gb|GE033494.1|GE033494
EST:     GCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGTAG                         TTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGTATTTTAATA
genomic: GCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTG-AGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGG-ATTTTAATA
EST: gi|207786833|gb|GD759240.1|GD759240
EST:     AACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCTACAGTAAATCCACGGCTGGATTTTAATATT
genomic: AACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
EST: gi|193500586|gb|FK464089.1|FK464089
EST:     TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
genomic: TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
EST: gi|207712306|gb|GD693770.1|GD693770
EST:     TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
genomic: TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
EST: gi|23734956|gb|BU765737.1|BU765737
EST:     TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCAACAGTA
genomic: TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTA
EST: gi|208116254|gb|GD914453.1|GD914453
EST:     ATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCAACAGTAAAT
genomic: ATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAAT
EST: gi|208060930|gb|GD857510.1|GD857510
EST:     CAACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
genomic: CAACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
EST: gi|208182235|gb|GD980248.1|GD980248
EST:     TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
genomic: TGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
EST: gi|15203048|gb|BI425816.1|BI425816
EST:     CAACGACAGGTTGAG                         TTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT
genomic: CAACGACAGGTTGAGgtatggatga ... catttgttagTTTTTGTCTATGAAACTTGCAACAGTAAATCCACGGCTGGATTTTAATATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAGgtatggatgaaaagcttatctccctattgcccacatgtgattcttaagtcatgtaactgatttgccctgtatgttctggttctgcaagctcagtgcaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcccta