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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATATACGAGCATGCTGTTGTCCTTAGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttcttgtcccttttttttcactctgaagacagctgaatctgcaaccaaagcaaacaatggacatcctctgattgttcacttaacataaacctg...

Basic information

species Glycine max
transcript GLYMA05G25730.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G25730.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g25420.2 (Oryza sativa), 5'ss of exon 3
ATATATACGAGCATGCTGTTGTCCTTAGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttcttgtcccttttttttcactctgaagacagctgaatc---tgcaaccaaagcaaacaatggacatcctctgattgttcacttaacataaacctg
| || || |||||||| ||||| || |||||||||| ||| || |||||||| ||||||||||| || |  ||  | || |||||||| |  ||| | |||| | ||    | | |  ||    ||| |      || |   | ||   || |  |          ||| || |  | |  |  || |  || ||| |   | 
ACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAGATGCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcctgtctacacttcacatcagttctgttaccgtatattcaattgtaggctgtcattttgatgcacgtaattt--tcttttatctaccattagttt-

upper sequence: GLYMA05G25730.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G121452_T01 (Zea mays), 5'ss of exon 3
ATATATACGAGCATGCTGTTGTCCTTAGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgt-aacttttcttgtcccttttttttcactctgaagacagctg--aatctgcaaccaaagcaaacaatggacatcctctgattgttcacttaacataaacctg
| || || ||||||||||||||  | |||||||||  |||||| |||||||| |||||| | ||||||| |||| ||||||||||||| |  ||| | |||| |  | ||  |  |||  ||| |  | | |     |   |   | | ||    | |           ||  || | ||||  |||    || | |||    
ACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATACATGgttagttctttgtcacccaatttgtcgattttatttgcctttattattttgatttctattttttaggctgaattcatgtgatgcttcgggcaataaaaag---

upper sequence: GLYMA05G25730.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G073077_T01 (Zea mays), 5'ss of exon 3
ATATATACGAGCATGCTGTTGTCCTT-AGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgt-aacttttcttgtcccttttttttcactctgaagacagctgaatctgcaaccaaagcaaacaatggac---atcc-tctgattgttcacttaacataaacctg
  || || ||||||||||||||  || |||||||||  |||||| |||||||| |||||| | |||||||  ||| | ||||||||||| |  ||| | |||| |  ||||  |  |||  ||| |  | | |     |   |    ||   |          |  | |||   |||| | ||||  ||    ||| | ||     
-CATTTATGAGCATGCTGTTGTTTTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATGGATACATGgttagttttttgtcacccaatttgtcgattttatttgcctttattactttgatttctaatttctttagactgaatccatgtgatgttttgagtaataaaa-----

upper sequence: GLYMA05G25730.1 (Glycine max), 5'ss of exon 3
lower sequence: AT1G64520.1 (Arabidopsis thaliana), 5'ss of exon 3
ATATATACGAGCATGCTGTTGTCCTTAGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttcttgtcccttttttttcactctgaagacagctgaatctgcaaccaaagcaaacaatggacatcctctgattgttcacttaacataaacctg
| || || |||||||||||||| || || || ||||  |||||||||||||||||||| || |||||||||||| |||| ||||| |||   |||||| |||||        |  ||   | |      ||||| |        |       |         ||   |  | || |   | | |||              
ACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaa---gaaccaactgt------ctgaacattatctttttcattttcttttggtctaacatatcttcttttcctctgcaccag-----------

upper sequence: GLYMA05G25730.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g02010.t01 (Vitis vinifera), 5'ss of exon 3
ATATATACGAGCATGCTGTTGTCCTTAGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttcttgtcccttttttttcactctgaagacagctgaatctgcaaccaaagcaaacaatggacatcct-ctgattgttcacttaacataaacctg--
||||||| ||||||||||||||||| ||||| || |  |||||||| ||||| ||||| ||||||||||| |||||||| ||||||||||||||| |  ||||| | ||  ||  |  |||    ||   |  |   || || || |  ||  ||    || |||  |  | || || |||       |    || | ||   
ATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGGATGCGTTTGAGAGGGATTTCTTTCAGTTGAAACCTTATTATACAGATACAGGgtaattctttctgctctgtttaagccatatttga---agttgcattttaaattaataataataattcaggtactgctaattaaaagagttctgtacagctcct

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|208078684|gb|GD876160.1|GD876160
EST:     AGTTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: AGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|192324155|gb|FK017886.1|FK017886
EST:     GATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: GATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|298178308|gb|HO024043.1|HO024043
EST:     GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|58022693|gb|CX709434.1|CX709434
EST:     GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCNTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|58019686|gb|CX706428.1|CX706428
EST:     GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTG                         CAATCGATTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|207833056|gb|GD801789.1|GD801789
EST:     GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|7234655|gb|AW569991.1|AW569991
EST:     GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|208241536|gb|GE036432.1|GE036432
EST:     TTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: TTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|33389688|gb|CA852895.1|CA852895
EST:     TTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: TTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|208066004|gb|GD865215.1|GD865215
EST:     TTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: TTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|58014496|gb|CX701238.1|CX701238
EST:     GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|193637559|gb|FK584498.1|FK584498
EST:     GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: GCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
EST: gi|208189714|gb|GD990950.1|GD990950
EST:     AGTTGAAGCCTTATTATACAGATGCCTG                         CAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT
genomic: AGTTGAAGCCTTATTATACAGATGCCTGgtaacttttc ... tttgttgcagCAATCGACTTCCACCATCTCCTCAGGAGTACCCAATTCTGGGTCTCAACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATATACGAGCATGCTGTTGTCCTTAGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttcttgtcccttttttttcactctgaagacagctgaatctgcaaccaaagcaaacaatggacatcctctgattgttcacttaacataaacctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG