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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactttgtattaccattatgtgttatagattatcgatgtaatgtcaatttatttctcccacttttttttgtttgattgtttttttactttttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGTTGATTCAAGTGACGTTGATAGGCTTGTGATAGCTAAGGAGGAGTTCCAT

Basic information

species Glycine max
transcript GLYMA13G01270.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G01270.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 4
cactttgtattaccattatgtgttatagattatc-gatgtaatgtc------aatttatttctcccacttttttttgtttgattgtt-tttttactttttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGTTGATTCAAGTGACGTTGATAGGCTTGTGATAGCTAAGGAGGAGTTCCAT
  |||||| |   |||    | |  ||||||||  ||  |  |  |      |   ||    |  ||| ||| | |     |||    | || || ||||     ||||||||| ||||| || |||||||||||||| || || || || |||||||| |||||||||||    ||||||||||| |  || || || ||||| |||
--ctttgt-taggcatggattctcttagattatttgacttccttccttttaaagactaggcatgacacgtttctctacgccattaacatattcacctttt-----tagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT

upper sequence: GLYMA13G01270.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 6
cactttgtattaccattatgtgttatagattatcgatgtaatgtcaatttattt-ctcccacttttttttgtttgattgtttttttactttttgtccat---agGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGTTGATTCAAGTGACGTTGATAGGCTTGTGATAGCTAAGGAGGAGTTCCAT
   |   ||| |  | |||     ||   || |  |||     |   || ||   ||   || |||  || |    |  | |  ||    | ||| |||   |||||||| ||| |||| ||||||||||| || || || || || ||||||||||||||||| ||    ||||||||||| | ||| || || || ||||||
---tgaatatcagaactata-accattacttttgcatgatgcattttttcatgaactaatacatttaattttccattaatatcattgtcatgtgtgcatttcagGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT
















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|193596299|gb|FK551304.1|FK551304
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|192319248|gb|FK009132.1|FK009132
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|192313159|gb|FK003279.1|FK003279
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|26047527|gb|CA784291.1|CA784291
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|207761436|gb|GD733765.1|GD733765
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|192299620|gb|FG990002.1|FG990002
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|7042626|gb|AW472520.1|AW472520
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|192306665|gb|FG998077.1|FG998077
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|12488647|gb|BG042170.1|BG042170
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|192326406|gb|FK017693.1|FK017693
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|10848119|gb|BF070667.1|BF070667
EST:     ATT-AGGTGGGCAAACAAGTATCAG                         GCCATATTTGGAG-TGTTACTTTCCAA-TACTTCA-GCATTA-TCTATTTT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATT-GGAGGTGTTACTTTCCAAATACT-CAAGCAATAATCTATGTT
EST: gi|15813778|gb|BI786053.1|BI786053
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACCCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
EST: gi|9565450|gb|BE474959.1|BE474959
EST:     ATTTAGGTGGGCAAACAAGTATCAG                         GCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT
genomic: ATTTAGGTGGGCAAACAAGTATCAGgtaaacactt ... ttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttatttctcccacttttttttgtttgattgtttttttactttttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGTTGATTCAAGTGACGTTGATAGGCTTGTGATAGCTAAGGAGGAGTTCCAT
                        gtttgat  putative branch site (score: 5)
                              ttgtttttttactttt  CT-rich tract
                ttttttttgtttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactttgtattaccattatgtgttatagattatcgatgtaatgtcaatttatttctcccacttttttttgtttgattgtttttttactttttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGTTGATTCAAGTGACGTTGATAGGCTTGTGATAGCTAAGGAGGAGTTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - tatgtgt