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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtattgatttaataaagaaaaattggaggctttcaacacagtaagttccacgtgtttttaattattaccattcatgttagaactggggactgtggagtgctttctagtgctatgacttgtttgataacaagaacatatttgtgggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGGTTCTACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATC

Basic information

species Glycine max
transcript GLYMA10G27890.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G27890.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 7
gtgagtattgatttaataaagaaaaatt----ggaggctttcaacacagtaagttccacgtgtttttaattattaccattcatgttagaactggggactgtggagtgctttctagtgctatgacttgtttgataacaagaacatatttgtgggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGGTTCTACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATC
|| | |  ||||||| |    || | ||    | | | |||  || || |         |  ||  | | | ||   ||||| |  |  | |    |     | |||  ||  |      || |   ||         |    | |||||  |||  |||||||| ||||||||||||||||| || || ||||||||||| ||||||||| || | |||||||| ||||||||||| || || ||| |||||||||| ||
gtaaat-ctgatttagtttgcaatatttttcagaaaggtttttactcattcttgatactgctttcctcaattttgg-attcaagaaactaatatttaaatgagggtgtattagaaattcctgtcaaattcaccttgctggttctttttgt--gttctgcagGAACCATATACAGCTCATCACTTTTTCCTAACCGAGCACCGCCTGGAAGGATTTTGCTCTTGAACTACATTGGAGGGGCTACCAATCCTGGAATTTTGTC
















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|192321103|gb|FK012443.1|FK012443
EST:     GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAG                         GAACTATATACAGCTCATCACCATTCCCCAACCGAGCACCACCTGGAAGGG
genomic: GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAGgtgagtattg ... ggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGG
EST: gi|5126795|gb|AI748531.1|AI748531
EST:     GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAG                         GAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGG
genomic: GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAGgtgagtattg ... ggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGG
EST: gi|192312907|gb|FK004049.1|FK004049
EST:     GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAG                         GAACTATATACAGCTCATCACTATTCCCCAACCGAGCGCCACC
genomic: GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAGgtgagtattg ... ggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACC
EST: gi|6094914|gb|AW119581.1|AW119581
EST:     GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAG                         GAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGG
genomic: GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAGgtgagtattg ... ggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGG
EST: gi|51342543|gb|CO983523.1|CO983523
EST:     GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAG                         GAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGG
genomic: GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAGgtgagtattg ... ggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGG
EST: gi|8284127|gb|BE021686.1|BE021686
EST:     GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAN                         GAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGAAAGGG
genomic: GAAGGGGTTTGGTCAATTGCATCCACGTAGCCAAGGAGTGGAAACATTAGgtgagtattg ... ggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGG
EST: gi|192298183|gb|FG991688.1|FG991688
EST:     GGAGTGGAAACATTAG                         GAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGG
genomic: GGAGTGGAAACATTAGgtgagtattg ... ggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttctagtgctatgacttgtttgataacaagaacatatttgtgggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGGTTCTACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATC
                       tgataac  putative branch site (score: 2)
                                 aacatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtattgatttaataaagaaaaattggaggctttcaacacagtaagttccacgtgtttttaattattaccattcatgttagaactggggactgtggagtgctttctagtgctatgacttgtttgataacaagaacatatttgtgggtttggcagGAACTATATACAGCTCATCACTATTCCCCAACCGAGCACCACCTGGAAGGGTTCTACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA