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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaacttacaactaaacatggctcattcctgtctggttccaaattcatacatcaaaagatttaatgatactgagatgttaaacatttccttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAGAGAAACT

Basic information

species Glycine max
transcript GLYMA18G44820.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G44820.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g26900.1 (Oryza sativa), 3'ss of exon 1
-------------------------------tacaacttacaactaaacatggctcattcctgtctggttccaaattcatacatcaaaagatttaatg-atactgagatgttaaac--atttccttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAGAGAAACT-
                               | |  | |   |  ||  || |||          |  |||||  | |        |  ||| |   |  | |    ||||   |    |||  | ||  | ||||||||||||||||||||||||| | ||  | || ||||| || |  ||| |    ||  
gtgagagggtttgggtttttccttttctttttcctccatgagaagaaggatagctagcgttgaattaattccatctgctcgatctgatcgatctctcgcgtgcgttcatgtccgatctgttttttcttttttcagGTGGAACAGTTGGAATCATTTCGGGTGCAACATCAACGAGAACACCATCCGGAGCACCG
















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|209711065|gb|BW676421.1|BW676421
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|193705157|gb|FK644059.1|FK644059
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|208072407|gb|GD869751.1|GD869751
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAA
EST: gi|192312271|gb|FK005275.1|FK005275
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|207783406|gb|GD758024.1|GD758024
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTCGGAATCATTTCGGCTGTCAAATTAACGAAAAAA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
EST: gi|151412992|gb|EV282800.1|EV282800
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GTTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|298193345|gb|HO033779.1|HO033779
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACACCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|207831467|gb|GD802557.1|GD802557
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATTA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|213596908|gb|DB964115.1|DB964115
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|208287148|gb|GE089250.1|GE089250
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAA
EST: gi|193651284|gb|FK599453.1|FK599453
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGA
EST: gi|208179904|gb|GD979297.1|GD979297
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|6481859|gb|AW201130.1|AW201130
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA
EST: gi|193452387|gb|FK421537.1|FK421537
EST:     ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGG                         GGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCG
genomic: ATTCAGGAGGAATCTGCTTGCTAATGGCCTTGGTAGAACTCCTCCAATGGggtaagtgtg ... ttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatacatcaaaagatttaatgatactgagatgttaaacatttccttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAGAGAAACT
              atttaat  putative branch site (score: 4)
                                      catttcctttt  putative PPT
         aaaagatttaatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaacttacaactaaacatggctcattcctgtctggttccaaattcatacatcaaaagatttaatgatactgagatgttaaacatttccttttggtgcaGGTGGAACAGTTGGAATCATTTCAGCTGTCAAATTAACGAAAAAATGATCAGAGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - -catggct
- - - - - - - - - - - - cattcct
- - - - - - - - - - - - - - - - - tggttcc
- - - - - - - - - - - - - - - - - - - - - - - catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatactg