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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAGgtaataaaacaaatgaattggagtgtaaatgtcacgcaagttttccttttttcactctgaattctgccctttaacattgtttatttgttaataatagctgcatttaacttttttggtggcacttgtacattttgttataaag

Basic information

species Glycine max
transcript GLYMA12G08600.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08600.1 (Glycine max), 5'ss of exon 15
lower sequence: LOC_Os10g34750.2 (Oryza sativa), 5'ss of exon 15
GTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAGgtaataaaacaaatgaattggagtgtaaatgtcacgcaagttttccttttttcactctgaattctgccctttaacattgtttatttgttaataatagctgcatttaacttttttggtggcacttgtacattttgttataaag
|| ||||||||||||||||| ||  ||| |||||| ||||| || ||||||||    || ||||| ||||||||||||||                    || |   | || |||     | || || |  | | |  ||   ||       |||  |||   || || |||||||   ||| |||                                  
GTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCTGCCAATGGTATAGTTGATCCGAACAAGgttg------------------gttttgctatc-cgccgtaatcccgttctgtagtatatat---gcatgagtgcatgattt---tgatactaatagccaaattgaaccag-------------------------------

upper sequence: GLYMA12G08600.1 (Glycine max), 5'ss of exon 15
lower sequence: GRMZM2G071304_T01 (Zea mays), 5'ss of exon 15
GTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAGgtaataaaacaaatgaattggagtgtaaatgtcacgcaagttttccttttttcactctgaattctgccctttaacattgtttatttgttaataatagctgcatttaacttttttggtggcacttgtacattttgttataaag
|| |||||||| ||||||||||| |||| ||| |||||||| || ||||||||    || ||||| ||||| || |||||                || |||     | |   |||          |   ||    || |     | | |   || || | || |      |  |||| | |  |                                   
GTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAGgt---------------ctgtagttc---ttttttgcattgccattcctccccatctcgattgtatacttctggtatagtatgttggaaggctaatgctgaaatcgaaccag------------------------------

upper sequence: GLYMA12G08600.1 (Glycine max), 5'ss of exon 15
lower sequence: Vv06s0061g00690.t01 (Vitis vinifera), 5'ss of exon 15
GTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAGgtaataaaacaaatgaattggagtgtaaatgtcacgcaagttttccttttttcactctgaattctgccctttaacattgtttatttgttaataatagctgcatttaacttttttggtggcacttgtacattttgttataaag--
|| ||||||||||||||||| ||| ||||||||||||||||||| ||||||||||| || ||||| ||||| ||||||||        |||| | ||| ||            ||   |||   | |||| |     ||   |     ||  | ||||| || | ||   |||  | |   || ||||  ||  |  |  |  |    ||| || | ||   
GTTTGGGAGGTGAAAGCTGCAGACTTGACCATTAGCCCTGTTCATCGTGCTGCAGTTGGAATAGTGGATCCTAACAAGgt-------taaat-atttgaag------------gcgcttttatgtatttttaa---aaaaaatataagttggctttgttcatatattgcaaattacagg--ttgacttactttatctcgttcatgtgctttcttttcaatag

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|208085609|gb|GD881541.1|GD881541
EST:     CCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG                         GGCATATCTCTACGATTTCCACGACTACTTCGAGTCAGGCCTGACAAAGCT
genomic: CCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAGgtaataaaac ... tgttataaagGGCATATCTCTACGATTTCCACGACTACTTCGAGTCAGGCCTGACAAAGCT
EST: gi|18040766|gb|BM309060.1|BM309060
EST:     CCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG                         GGCATATCTCTACGATTTCCACGACTACTTCGAGTCAGGCCTGACAAAGCT
genomic: CCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAGgtaataaaac ... tgttataaagGGCATATCTCTACGATTTCCACGACTACTTCGAGTCAGGCCTGACAAAGCT
EST: gi|51342409|gb|CO983482.1|CO983482
EST:     CCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG                         GGCATATCTCTACGATTTCCACGACTACTTCGAGTCAGGCCTGACAAAGCT
genomic: CCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAGgtaataaaac ... tgttataaagGGCATATCTCTACGATTTCCACGACTACTTCGAGTCAGGCCTGACAAAGCT
EST: gi|51338234|gb|CO982100.1|CO982100
EST:     CCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG                         GGCATATCTCTACGATTTCCACGACTACTTCGAGTCAGGCCTGACAAAGCT
genomic: CCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAGgtaataaaac ... tgttataaagGGCATATCTCTACGATTTCCACGACTACTTCGAGTCAGGCCTGACAAAGCT
EST: gi|151394051|gb|EV263922.1|EV263922
EST:     GTGGGCATGGTAGATCCGAACAAG                         GGCATATCTCTACGATTTCCACGACTACTTCGAGTCAGGCCTGACAAAGCT
genomic: GTGGGCATAGTAGATCCGAACAAGgtaataaaac ... tgttataaagGGCATATCTCTACGATTTCCACGACTACTTCGAGTCAGGCCTGACAAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAGgtaataaaacaaatgaattggagtgtaaatgtcacgcaagttttccttttttcactctgaattctgccctttaacattgtttatttgttaataatagctgcatttaacttttttggtggcacttgtacattttgttataaag

- - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG