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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaactttagttaacataggatttcagtgaatagtaaaatgatttgttcaacctcttaagaatataccctttgtatttttgacag

Basic information

species Glycine max
transcript GLYMA07G03260.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03260.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os04g55180.1 (Oryza sativa), 5'ss of exon 10
ACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaacttta-gttaacataggattt--cagtgaatagtaaaatgatttgttcaacctcttaagaatat--accctttgtatttttgacag-------------------------------------------------------------------------------
||||||| |   |  | || ||| |||| |||||||| ||||| |||   ||  |  |  |    ||||||||||||||||||||||| ||||||||||||||| |   |||    || |  || ||||      ||   ||    ||     ||    ||| ||     ||     |||      ||||||                                                                                 
ACTTGCCACTCCCCATAGCTGAGGAGTTCCAGAAAGGTAATCCTGCAGCCATAAAATTGGAGCCAATAGAAGGAGCTGGTCATATGCCTCAAGAGGACTGgtaattgtttttttactagctcagtattttctgtcgatctgtgtcctgtaaaatttgtactcatagttccatcggtgcttgcctgctttgacgtgtaaccttcaacctttaccttttggccaattcatatacttgtgcgatccttaacgcatctcacttgtcatgttatgcag

upper sequence: GLYMA07G03260.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G117531_T04 (Zea mays), 5'ss of exon 10
ACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaactttagttaacataggatttcagtgaatagtaaaatgatttgttcaacctcttaagaatataccctttgtatt---tttgacag----------------------------------------------------------------------
|||| || |  ||  | || ||| | ||  || |||  ||||| |      |  | ||  |   |||||||||||||||||| ||||| ||||||||||||||| |   || ||       | |  |||||  |||  |||  |  |   | ||   | ||   |  ||| | |||  ||    ||| ||                                                                        
ACTTACCGCTCTCGATAGCTGAGGAATTCAAGCAAGCTAATCCTGGCGTTGTAAAACTAGAGGCGATAGAAGGAGCTGGTCACATGCCGCAAGAGGACTGgtaactgttttcagaagcttgatgggttcagccaat--taacgtt-tacatacagtttttttttagaataacgtttacatacagtttcacgaattaaaagctgtgtacatccactaccctttagactttgtacatccttgacgcatctcacatcatctgcag

upper sequence: GLYMA07G03260.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv09s0002g07500.t01 (Vitis vinifera), 5'ss of exon 10
ACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaactt-tagttaacataggatttcagtgaatagtaaaatgatttgttcaacctcttaagaatataccctttgtatttttgacag
|  |||| || || ||||||||  ||||||| || ||||| || |   | ||  | ||||| ||||||||||| ||||||||||||||||| |||||||||||| | |||| |   |  |||   || | ||| ||   ||   |    | || ||| | |||| | |||||  |||       || |||
ATCTGCCTCAATCAGTGGCAGAAGAGTTTCAAAAGGGAAACCCTGATTATATAAAACTTAAGTTGATAGAAGGTGCTGGTCATATGCCACAGGAGGACTGgtaattcacttctgaattgcattt-atgttagttaagcttacttttgcct-tttaactttttaacagtatactgttt-------tggcag

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|31312540|gb|CD397743.1|CD397743
EST:     ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
EST: gi|31472542|gb|CD414570.1|CD414570
EST:     ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATCCCACAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
EST: gi|5510083|gb|AI856467.1|AI856467
EST:     ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
EST: gi|209727722|gb|BW658459.1|BW658459
EST:     ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
EST: gi|31466823|gb|CD408851.1|CD408851
EST:     ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
EST: gi|16342366|gb|BI967961.1|BI967961
EST:     ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATAT-CCACAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
EST: gi|31476274|gb|CD418302.1|CD418302
EST:     TCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACTAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: TCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCAC-AAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
EST: gi|209703109|gb|BW673294.1|BW673294
EST:     ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
EST: gi|5510381|gb|AI856698.1|AI856698
EST:     ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
EST: gi|31463415|gb|CD405443.1|CD405443
EST:     ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
EST: gi|31466761|gb|CD408789.1|CD408789
EST:     ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTG                         GCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT
genomic: ATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaact ... tttttgacagGCCTGAGAAAGTTGTTGATGCTTTCAGAATGTTCTTCTGATTTCAACAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAGCTTAAATTGATAGAAGGAGCTGGTCATATGCCACAAGAGGACTGgtaagtaactttagttaacataggatttcagtgaatagtaaaatgatttgttcaacctcttaagaatataccctttgtatttttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA