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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGAACTTGGGGGTCTCAAAAGTGATCAGGGCTGATCAGAAAAGATTCTTCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtcattatctctgtccttttttcctttttttttttatatattgtgggaagaggaatttttgctgtaaattcttgctatctcatcgcag

Basic information

species Glycine max
transcript GLYMA20G03020.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G03020.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G32080.1 (Arabidopsis thaliana), 5'ss of exon 4
TGGGAACTTGGGGGTCTCAAAAGTGATCAGGGCTGATCAGAAAAGATTCTTCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtcattatctctgtccttttttcctttttttttttatatattgtgggaagaggaatttttgctgtaaattcttgctatctcatcgcag
 || |     || || || ||||| ||||| ||||| |||||| | ||||||||||||||||||| |||||| ||||| ||||||||||| |||||||||||   ||      |   |  || |||  |   || | | || | |  ||||    |      ||||  |  ||||   ||    |||||    ||
CGGAATGACTGGTGTTTCTAAAGTAATCAGAGCTGACCAGAAACGGTTCTTCTTTGATCTTGGGAACAATAACAGGGGCCATTTCTTAAGGATATCTGAGgtaatct--tggaagaacaatcttttgctggcttatctcttgagagcttgtatttaccatggttttaacattaaagcatt----tctcaatatag

upper sequence: GLYMA20G03020.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0004g00040.t01 (Vitis vinifera), 5'ss of exon 3
TGGGAACTTGGGGGTCTCAAAAGTGATCAGGGCTGATCAGAAAAGATTCTTCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtca--ttatctct-----gtccttttttcctttttttttttatata---ttgtgggaagaggaa--tttttgctgt-------aaattcttgctatctcatcgcag--------------
||| ||||||||||||||||||||||| || |||||||| || || ||||||||||||||||| ||||| || |||||||||||| |  | |||||||||||||| | | |  |  | | |     |  | |       |  ||| || || ||   |||    |  | |||  ||| |  ||        ||||||    ||| |       |              
TGGTAACTTGGGGGTCTCAAAAGTGATTAGAGCTGATCAAAAGAGGTTCTTCTTTGATCTTGGTAGCAACAACAGGGGTCATTTCCTGCGGATATCTGAGgtgtgttttaagatggtttttaaagagagcctaaaaaaataatttattcatgtagttttgcaccataatgaaggtttctaatggcaatttaaaattccaattatttttaaatggcaccatgattgcag
















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|254344654|gb|GR851244.1|GR851244
EST:     TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAG                         GTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGG-CTCAAG
genomic: TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtc ... ctcatcgcagGTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
EST: gi|7234734|gb|AW570068.1|AW570068
EST:     TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAG                         GTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
genomic: TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtc ... ctcatcgcagGTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
EST: gi|6070564|gb|AW099951.1|AW099951
EST:     CTTTGATCTTGGGAGCCATAATAGGGGTCATTTTCTTAAGACTATCTGAG                         GTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
genomic: CTTTGATCTTGGGAGCAATAATAGGGGTCATTT-CTTAAGAATATCTGAGgtgtgctgtc ... ctcatcgcagGTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
EST: gi|254325803|gb|GR838684.1|GR838684
EST:     TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAG                         -TTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGG-CTCAAG
genomic: TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtc ... ctcatcgcagGTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
EST: gi|15664854|gb|BI702225.1|BI702225
EST:     TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAG                         GTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
genomic: TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtc ... ctcatcgcagGTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
EST: gi|254344653|gb|GR851243.1|GR851243
EST:     TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAG                         GTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
genomic: TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtc ... ctcatcgcagGTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
EST: gi|22929538|gb|BU546677.1|BU546677
EST:     TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAG                         GTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
genomic: TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtc ... ctcatcgcagGTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
EST: gi|9203424|gb|BE329577.1|BE329577
EST:     TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAG                         GTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
genomic: TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtc ... ctcatcgcagGTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
EST: gi|192304816|gb|FG996032.1|FG996032
EST:     TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAG                         GTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG
genomic: TCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtc ... ctcatcgcagGTTGCGGGTTCTGATAGATCCTCCATTATTCTTCCCCTGTCAGGGCTCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGAACTTGGGGGTCTCAAAAGTGATCAGGGCTGATCAGAAAAGATTCTTCTTTGATCTTGGGAGCAATAATAGGGGTCATTTCTTAAGAATATCTGAGgtgtgctgtcattatctctgtccttttttcctttttttttttatatattgtgggaagaggaatttttgctgtaaattcttgctatctcatcgcag

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