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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagatgtctataaaattttttacacgaattattctcatttcatataaattgttgtggcaaatgaatgtaactgtaatgattttatagaatcagca...

Basic information

species Glycine max
transcript GLYMA10G43230.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 5'ss of exon 19
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagatgtctataaaattttttacacgaattattctcatttcatataaattgt-tgtggcaaatgaatgtaactgtaatgattttatagaatcagca--------
 || |||||||||||||| ||||| |||||||| ||||| ||||||||||||||||||||||||||||| ||||||||| | ||||| ||||| || |||||    || |      |  |   |||     | |||||| | || |   |||   || | | || ||| | |||     |  |  || |  |  | |   |        
AGACCCACTTAGTGTTTCGGTTGCAATTCTTCACCAGTTTAACATTTTGCCTGAGATGTATCAAGTTGGGTACACAAAATTGTTCTTTCGAACTGGCCAGgtg---agcta-----agcagcctttgttttatttattcac-ttcctggtaatgagtgtattgccaataactgttggccttgtttttctgaatgagcgttaaatgtttg

upper sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 19
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagatgtctataaaatttttta-cacgaattattct--catttcatataaattgttgtggcaaatgaatgtaactgtaatgattttatagaatcagca-----------------------------------------------------------------------------------------
 |||||||| |||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||  | ||||||||||| || ||||| ||    ||| |||  | |||  |  ||    | |   |   |  | |    | |||||     | |||  | ||          | || | || |    |                                                                                         
AGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTTGGCTACACAAAGTTGTTCTTCCGAACTGGTCAGgt-tagttctgtttattcagtttcctggcaatggtcacattagaaactgaagctatttgtttcattacatgtttatagaccattcattgttctggattttttaccattatatgtatgcacgaccttttttatttgttaagcatttggtgaaagtgatcttgtgttactgtgtcctttgatattgggctgaag

upper sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 19
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagatgtctataaaattttttac--acgaattattctcatttcatataaattgttgtggc-aaatgaatgtaactgtaatgattttatagaatcagca-----------------------------------------------------------------------------------------
 |||||||| |||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||  | ||||||||||| || ||||| ||    | | |||  |||||| | |  | |      |   |    | ||  |||| | |    | |||  | ||     | | ||| | | | ||    |                                                                                         
AGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTTGGCTACACAAAGTTGTTCTTCCGAACTGGACAGgt-tagttctatttattcaattttctgccaatggccacattagaaactaaatctattgctttcattacatgtttatagac-cattcattgtcttggatttttatctatatatgtatgtactattttatttttgttttaagcatttggtgaaactaatcttgtgttactttgtccttcgatattgggctgaag

upper sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 18
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 5'ss of exon 23
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagatgtctataaaattttttacacgaattattctcatttcatataaattgttgtggcaaatgaatgtaactgtaatg-attttatagaatcagca
                    |||| ||||| |||||||| || || ||||| ||||||||||||||||||||||||||  | || ||| |||| || |||||||  |   |  | |        |      ||  | | | |||| |||           ||||   ||||   | | | |||    ||  ||        
--------------------TTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAGgtat--aatagcttgtcgg----ctggtgtcaaagacttttattttataagg--------ggcag--gaataagagtctcatgtgcattgcag--------

upper sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 18
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 5'ss of exon 20
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagatgtctataaaattttttacacgaattattctcatttcatataaattgttgtggcaaatgaatgtaactgtaatg-attttatagaatcagca
 ||||| || |||||||||||||| ||||| |||||||| || || ||||| ||||||||||||||||||||||||||  | || ||| |||| || |||||||  |   |  | |        |      ||  | | | |||| |||           ||||   ||||   | | | |||    ||  ||        
AGATCCTCTAAGTGTTTCAGTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAGgtat--aatagcttgtcgg----ctggtgtcaaagacttttattttataagg--------ggcag--gaataagagtctcatgtgcattgcag--------

upper sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 18
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgta-tatagatgtctataaaattttttacacgaattattctcatttcatataaa-ttgttgtggcaaatgaatgtaactgtaatgattttatagaatcagca
 ||||| || |||||||| ||||| ||||| |||||||| || || ||||| |||||||| |||||||||||||||||| | || ||| |||| || |||||| ||||  |     |   || | ||      |     | ||  | | | |   ||  ||  | | |      | ||  |                     
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactataactagtcgtctgatgtcttgactttaggggccacaaattagacattcttactgcagtatacttgcttcaccattgcag----------------

upper sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 18
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagatgtctataaaattt---tttacacgaattattctcatt---tcatataaattgttgtggcaaatgaatgtaactgtaatgattttatagaatcagca
 ||||||||||||||||||||||| || |||||||||||||| ||| |||||||||||||||||||||||||||||||| | || |||||||| || |||||     || ||   ||  || |    |  ||   | ||   | |||    |  || | |||| |  | |||  ||||| ||| |  | |   || |   ||    
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaa---taaatgctct---

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|23055983|gb|BU577699.1|BU577699
EST:     CTGAGATGTATCAAGTTGGCTACACGAAACTATTCTTTCGAACAGGGCAG                         ATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTACGT
genomic: CTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagat ... gtgattgcagATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGT
EST: gi|19934507|gb|BQ079537.1|BQ079537
EST:     CTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAG                         ATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGT
genomic: CTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagat ... gtgattgcagATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGT
EST: gi|193513350|gb|FK471458.1|FK471458
EST:     CTGAGATGTATCAAGTTGGCTACNCAAAACTA-TCTTCCGAACAGGGCAG                         ATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGT
genomic: CTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagat ... gtgattgcagATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGT
EST: gi|18039602|gb|BM307896.1|BM307896
EST:     CTGAGATGTATCAAGTTGGCTACACGAAACTATTCTTTCGAACAGGGCAG                         ATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTACGT
genomic: CTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagat ... gtgattgcagATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGT
EST: gi|193715297|gb|FK652072.1|FK652072
EST:     CTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAG                         ATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGT
genomic: CTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagat ... gtgattgcagATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGT
EST: gi|193570175|gb|FK523972.1|FK523972
EST:     TTCTTCCGAACAGGGCAG                         ATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGT
genomic: TTCTTCCGAACAGGGCAGgtatatagat ... gtgattgcagATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagatgtctataaaattttttacacgaattattctcatttcatataaattgttgtggcaaatgaatgtaactgtaatgattttatagaatcagca

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