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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtcatttatctttccagattatgcataacctattgtacaaaccattcttatttcaacaacaaatgttttttgaaatgaaatttgtttgctaattatctgtttcag

Basic information

species Glycine max
transcript GLYMA10G35230.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 5'ss of exon 4
GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtcatttatctttccagattatgcataacctattgtacaaaccattcttatttcaacaacaaatgttttttgaaatgaaatttgtttgctaattatctgtttcag-----------------------------------------------------------------------------
|| |||||||| || || |||||||| |||||| | ||  || | || || |||||||| ||||||||||||||||||||||||||||| ||||||||  |     |||        |||||   ||   |    || ||  |     |||  ||   |  |     ||| || |      |||| ||   |  | |||  ||||                                                                              
GTGACTGTTGGTGCATCATTTTTGTCACAAACATTGGCGTTGGAGGATTCCACAACAGTAAAGTTTGAAATATGGGATACTGCTGGTCAGGAGAGgtgcataaatattagaagctttgattaactattttcccaagtgcatccttgcattaactctgtactatggaatttctgtaccatcttttgcttcacatatgtcttcttcacccttgatttacattgtttgcaagcatatgtgttgctattcgttaccaaagaagtcacgagaactggttaattttcag

upper sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 4
GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtg-actgtcatt--tatctttccagattatgcataacctattgta----caaaccattcttatttcaacaacaaatgttttttgaaatgaaatttgtt-tgctaattatctgtttcag-----------------------------------------------------------------------------
|||||||| || || || ||||| || |||||| | ||| || | ||||| |||| ||| || ||||||||||||||||| ||||| ||||||||||  ||   ||    |||  ||  || || | |  | | |    ||    ||  |  ||  |   | |  | ||   ||||| ||| |      | ||  |     |||    |||                                                                                
GTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCAACAATAGTGAAATTTGAAATATGGGATACCGCTGGACAAGAGAGgtacacatacagcactatggttttagcttcttccaatcttgggataatggcatgctgttggtgcattagaagcattggttttgtgagaaagttctagtagtatgtgttactgatttttacaattgatccatcttacgtgccacacatgcatatggtttttctcaatcaagaactcattggtaccagccaattttag

upper sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 5
GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgact-gtcattt--atctttccagattatgcataacctattgtacaaaccattcttatttcaacaacaaatgttttttgaaatgaaatttgtttgct--aattatctgtttcag-----------------------------------------------------------------------
||||||||||| || |||||||| || |||||| | ||  || | || || |||| ||| ||||||||||| |||||||||||||| |||||||||| | | |    |   |||  | |  ||| || ||| |  ||||   | ||  | |       | | |||    ||| |   | |    ||||     |  |   |||| | |  |                                                                       
GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggtgctgagatcagtacttattttggatacctaattggg-atactttgccgcacgtacccacagg-atttctgatagtattctttgcacatttgatccatctttctttgcaagcacaacagcacatgcatgtttttgcctgaatcaagagtcatgagaattgagagcttgtcaatttcag

upper sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 4
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 4
GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtcatttatctttccagattatgcataacctattgtacaaaccattcttatttcaacaacaaatgttttttgaaatgaaatttgtttgctaattatctgtttcag
|||||||||||||| || || ||||| ||||| |||||  ||||||||||||| ||||| |||||||||||||||||||| || || || |||||||     | |    |   | |||||| || ||  | |||| ||  |   |  |   || |||          ||  |   ||  ||  ||  | |   ||||   ||| ||
GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgtat---taaacccttcatgcagatt-tgtattgcttattttattagataaacgctttgcaa--------acttactaggatttaacctgcattcactttat---ttttag

upper sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 4
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 4
GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgt-------gactgtcatttatctttccagattatgcat--aacctattgtacaaaccattcttatttcaacaacaaatgttttttga---aatgaaatttgtttgctaat-tatctgtttcag---------------------------------------------
|| ||||| |||||||| || ||||| |||||||| ||  ||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||||       | |   |  || | ||||| | | |   ||   || |  |  |   |  |    ||  |||||    | | || ||      | ||||||   | |     | | ||| || ||                                              
GTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattggccaacccattttttttcctgttcacctatctgactttctaaattcaatagaaataactcaacttatagtcttcttgagtctattgaaatggatctagagctctctctcttccatgaaaacccatttgagaaaattacagaggataacttcattcctcag

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|5605755|gb|AI899819.1|AI899819
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|193543327|gb|FK502506.1|FK502506
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTAT
EST: gi|208204745|gb|GE006542.1|GE006542
EST:     TTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: TTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|15813084|gb|BI785359.1|BI785359
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|308098577|gb|HO760318.1|HO760318
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|298165609|gb|HO011658.1|HO011658
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|298183380|gb|HO028593.1|HO028593
EST:     GACTCTACAACAGTCAAGTTTGGAATATGGGATACTGCTGGTCAGGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|7286166|gb|AW598653.1|AW598653
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|298177777|gb|HO027330.1|HO027330
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|298182667|gb|HO031402.1|HO031402
EST:     GACTCTACAACGGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|15201204|gb|BI424748.1|BI424748
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|298174351|gb|HO017687.1|HO017687
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtca ... tctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtcatttatctttccagattatgcataacctattgtacaaaccattcttatttcaacaacaaatgttttttgaaatgaaatttgtttgctaattatctgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA