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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatatatattttttcttattagtaccttagttttctatattcactgtgccattgaaagaattgcccaacacttcttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTGCTTGGTGGTACCCTTGTTCCATACTACCTTGAAGAGACAGCAAATTGGG

Basic information

species Glycine max
transcript GLYMA02G04320.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04320.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G70580.2 (Arabidopsis thaliana), 3'ss of exon 6
--------------gtaatatatatattttttcttattagtaccttagttttctatattcactgtgccattgaaagaattgcccaacacttcttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTGCTTGGTGGTACCCTTGTTCCATACTACCTTGAAGAGACAGCAAATTGGG
               | | ||  | |||| ||     | |||  |  ||||| ||   |   | |    | | |     |  | |    |  |  ||| |||||| |||||||||| ||||| || ||||||||||| || || ||  ||||| | |||||||| |||||||| ||||| ||||||||| | | ||| ||||
ttgatggctaagagttcagattcagatttcttgcagatggta--taggttttttaggcttggtttatagtagcatctggtcacaagttttcttggttggcagATTCTGGTTCCAGTTCCACAGTATCCACTCTACTCGGCTACTATATCTCTGTTAGGTGGTACTCTTGTTCCTTACTATCTTGAAGAGTCTGAAAACTGGG
















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|17518503|gb|BM187545.1|BM187545
EST:     TCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: TCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|120490920|gb|EH219087.1|EH219087
EST:     AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACA-TTGCTCTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|13125648|gb|BG316218.1|BG316218
EST:     GTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: GTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|14999822|gb|BI320636.1|BI320636
EST:     AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|20497810|gb|BQ272740.1|BQ272740
EST:     AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAACAACAATTGCTCTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|120531769|gb|EH259902.1|EH259902
EST:     AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|193383290|gb|FK348643.1|FK348643
EST:     ATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: ATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|120530295|gb|EH258429.1|EH258429
EST:     AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|37996526|gb|CF808115.1|CF808115
EST:     AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|213594062|gb|DB961950.1|DB961950
EST:     AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTG
EST: gi|13562529|gb|BG550749.1|BG550749
EST:     AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|120495797|gb|EH223964.1|EH223964
EST:     AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|20448749|gb|BQ252873.1|BQ252873
EST:     GTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: GTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|192313436|gb|FK005516.1|FK005516
EST:     AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|6566266|gb|AW233945.1|AW233945
EST:     GTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: GTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|22522287|gb|BU081107.1|BU081107
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGGgtaatatata ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctatattcactgtgccattgaaagaattgcccaacacttcttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTGCTTGGTGGTACCCTTGTTCCATACTACCTTGAAGAGACAGCAAATTGGG
                                         cttcttatt  CT-rich tract
      tatattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatatatattttttcttattagtaccttagttttctatattcactgtgccattgaaagaattgcccaacacttcttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTGCTTGGTGGTACCCTTGTTCCATACTACCTTGAAGAGACAGCAAATTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA