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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGCATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgcacaaatagtaaaaaattgtgtgcaacaagatgaatagacatgctcatgttatttattatctatatattctctggcctctgcatctttcttattgcatgcaagcaattattttatcatccgctccacttggtaatggaaaagcttaaaggattcttgttggcttcag

Basic information

species Glycine max
transcript GLYMA05G02190.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 6
AGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGCATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgcacaaatagtaaaaaattgtgtgcaacaagatgaatagacatgctcatgttatttattatctatatattctctggcctctgcatctttcttattgcatgcaagcaattattttatcatccgctccacttggtaatggaaaagcttaaaggattcttgttggcttcag
||||||| | ||||| || ||||||||||| ||||| ||||| || ||||| || || ||||||||||| |||||||| || || ||||| || |||||||||      |||| | | ||||   ||   || ||| |  |  |      |  || || |||   ||   | ||   |        ||||   | | || |  |  |||                                                                   
AGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGCACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAGgtac-----cacagaaaataaa---ttacctgtaactaattttacttggttcatc-tgatataagtttggtgtaaggttgtgatagtctggtacgtactcaacgt-tgcc------------------------------------------------------------------

upper sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 6
AGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGCATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgcacaaatagtaaaaaattgtgtgcaacaagatgaatagacatgctcatgttatttattatctatatattctctggcctctgcatctttcttattgcatgcaagcaattattttatcatccgctccacttggtaatggaaaagcttaaaggattcttgttggcttcag
||||||| | ||||| || ||||||||||| ||||| ||||| || || || || || ||||| |||||||||||||| || || ||||| || ||||||||||     ||||||  ||  |    | | |||| | |  |   || |  |  |  ||||||  ||  |   | ||   |  ||    | |||  |   | | |                                                                        
AGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAACACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaa---ctcacaaaatgtttacttgtttctgcagctatcttt-taaattttttattgttatgcatatttggtgtaaagttgggaaagtacatgctggctttgg------------------------------------------------------------------------

upper sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 5'ss of exon 6
AGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGCATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgcacaaatagtaaaaaattgtgtgcaacaagatgaatagacatgctcatgttatttattatctatatattctctggcctctgcatctttcttattgcatgcaagcaattattttatcatccgctccacttggtaatggaaaagcttaaaggattcttgttggcttcag
||||||||| || || || |||||||| || ||||| |||||  | || ||||||||||| || ||||| || |||||||||||||||||||| |||||||||      |||||||   | | ||||  || |  |||  |  |||   |       |||  |  | ||  |  |           ||  | |||  |   |||  || ||    || ||||||  | | ||                                            
AGAGACATTAATCGCAGGTGGTCCTTTCGTGCTTCCGCTTGCCAACAAACATAATGTAAAGATTCTTCCGGCAGATTCAGAACATTCTGCCATATTTCAGgtat-----cacaaatcacatagaattaagtacctcaactttcatattgagttcagcgttggtcttaatgcaagt-----------tcaacctctggcaatttgagtgaaaaatcttcttttat-gttctctag------------------------------------------

upper sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 5'ss of exon 6
AGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGCATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgcacaaata-gtaaaaaattgtgtgcaacaagatgaatagacatgctcatgttatttattatctatatattctctggcct-ctgcatctttcttattgcatgcaagcaattattttatcatccgctccacttggtaatggaaaagcttaaaggattcttgttggcttcag
||||||  | |||||||| ||||||||||| ||||||||||| || ||||| |||||||| || ||||| ||||| |||||||| ||||| || ||||||||| | | ||| |  ||     | |  |   |  | |      | |   ||||   ||  | |  | |   ||||| ||   |    | ||| ||  |  ||                                                                            
AGAGACCCTAATTGCTGGGGGTCCTTTTGTCCTTCCTCTTGCACACAAGCACAATGTAAAGATCCTTCCTGCTGACTCAGAACACTCTGCAATATTTCAGgtagggaagcatatctacactgatagctaattttagcttttcaatt---catgtgtattgtgtacaatgcatatatgttaattataatgctggattatctttg---------------------------------------------------------------------------

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|254347803|gb|GR854052.1|GR854052
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|193522059|gb|FK482618.1|FK482618
EST:     TAATTGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: TAA-TGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|193710747|gb|FK641760.1|FK641760
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|193677377|gb|FK615307.1|FK615307
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|254343989|gb|GR857745.1|GR857745
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|193399209|gb|FK361743.1|FK361743
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|17401027|gb|BM177809.1|BM177809
EST:     GTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: GTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|193691933|gb|FK631016.1|FK631016
EST:     ATAATGT-AAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|9259629|gb|BE347776.1|BE347776
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTANGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|207685213|gb|GD668559.1|GD668559
EST:     CTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAG
genomic: CTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAG
EST: gi|15589848|gb|BI674464.1|BI674464
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|16278852|gb|BI943128.1|BI943128
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|10846631|gb|BF069467.1|BF069467
EST:     TAATGTATGAATTCTTTCC-GCTGATTCAGAACATTCTGTCATTTTT-AG                         TGTATCGCAGGG
genomic: TAATGTAAAAATACTT-CCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATC-CAGGG
EST: gi|193518771|gb|FK472744.1|FK472744
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|209718278|gb|BW657870.1|BW657870
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|16277944|gb|BI942645.1|BI942645
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
EST: gi|193306271|gb|FK271390.1|FK271390
EST:     ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAG                         TGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA
genomic: ATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgc ... ttggcttcagTGTATCCAGGGGTTGCCAGAGGGTGCACTTAGGAGAGTTATTTTAACTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGCATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgcacaaatagtaaaaaattgtgtgcaacaagatgaatagacatgctcatgttatttattatctatatattctctggcctctgcatctttcttattgcatgcaagcaattattttatcatccgctccacttggtaatggaaaagcttaaaggattcttgttggcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT