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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatatctttcatgatcctataattacatatttttttggttttccatcatgcattcttgttaggaagaagaaattgtatttttgatgttgtattttatgctacttgctcttattagGGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCCAAGTTGTTAGAGATGCTAAAAGTTTGGGGTATACTGAACCAG

Basic information

species Glycine max
transcript GLYMA20G11950.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G11950.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G21060.3 (Arabidopsis thaliana), 3'ss of exon 6
gtatatatatctttcatgatcctataattacatatttttttggttttccatcatgcattcttgttaggaagaagaaattgtatttttgatgttgtattttatgctacttgctcttattagGGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCCAAGTTGTTAGAGATGCTAAAAGTTTGGGGTATACTGAACCAG
                   |      | | || || ||| | |||||   || |       | |  | | | |  | || | |   |    ||||||     | |      |  |  |||| || ||||| ||||||||||||||| |||||||||| |||||  | ||||||||||||  || ||| ||||   ||||||| ||||||||||
------------------gtaagcagacttcagatgtttatcgtttt---tcttatcccaatatatgcatgtattatttatttacgtatctttgtatcc---gttctcgattaatgatagGTACCTTGGGATATGTAATGAGTGAGCTTGAAGATGGCAAGCCTCTAAGCCAAGTTGTTCAAGCTGCCAAAAAGCTGGGGTACACTGAACCAG

upper sequence: GLYMA20G11950.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0009g01460.t01 (Vitis vinifera), 3'ss of exon 5
gtatatatatctttcatgatcctataattacatatttttttggttttccatcatgcattcttgttaggaagaagaaattgtatttttgatgttgtattttatgct-acttgctctt--attagGGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCCAAGTTGTTAGAGATGCTAAAAGTTTGGGGTATACTGAACCAG
                           |    ||     ||| || |  |      ||  |||| |||     | |||   | || | || || |  || |  || |||   | ||  | |||| || ||||| ||||| ||||||||||| |||| |||||||||||| || ||||||||||  ||||| ||||| ||||| |||||||||||||
--------------------------gtattttaaggcattgattctatagagcatatctttgtaaggtgtgtgcaatatcagttctaatatt-tgcttcacactcactcatttttgaaatagGCACTTTGGGATATGTGATGAGTGAGGTCGAAGGTGGAAAGCCATTCAGTCAAGTTGTTAAGGATGCCAAAAGCTTGGGCTATACTGAACCAG
















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|9899975|gb|BE608943.1|BE608943
EST:     CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCG                         GGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCC
genomic: CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCGgtatatatat ... ctcttattagGGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCC
EST: gi|193539305|gb|FK497715.1|FK497715
EST:     CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCG                         GGACATTGGGTTATGTAA
genomic: CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCGgtatatatat ... ctcttattagGGACATTGGGTTATGTAA
EST: gi|193727061|gb|FK660275.1|FK660275
EST:     CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCG                         GGACATTGGGTTATGTAA
genomic: CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCGgtatatatat ... ctcttattagGGACATTGGGTTATGTAA
EST: gi|193721822|gb|FK658306.1|FK658306
EST:     CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCG                         GGACATTGGGTTATGTAA
genomic: CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCGgtatatatat ... ctcttattagGGACATTGGGTTATGTAA
EST: gi|193711761|gb|FK647860.1|FK647860
EST:     CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCG                         GGAACATTGGGTTATGTAA
genomic: CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCGgtatatatat ... ctcttattagGGA-CATTGGGTTATGTAA
EST: gi|298178813|gb|HO024548.1|HO024548
EST:     CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCG                         GGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCC
genomic: CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCGgtatatatat ... ctcttattagGGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCC
EST: gi|18040511|gb|BM308805.1|BM308805
EST:     CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCG                         GGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCC
genomic: CATAATCTCTTCTGGTGATCCCGTTCATCAAATTATTGGGAGTTTGAGCGgtatatatat ... ctcttattagGGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggaagaagaaattgtatttttgatgttgtattttatgctacttgctcttattagGGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCCAAGTTGTTAGAGATGCTAAAAGTTTGGGGTATACTGAACCAG
                  ttttgat  putative branch site (score: 4)
                                         cttgctctt  putative PPT
         aaattgtatttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatatctttcatgatcctataattacatatttttttggttttccatcatgcattcttgttaggaagaagaaattgtatttttgatgttgtattttatgctacttgctcttattagGGACATTGGGTTATGTAATGAGTGAGGTTGAAGATGGAAAGCCATTGAGCCAAGTTGTTAGAGATGCTAAAAGTTTGGGGTATACTGAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG