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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGATATATTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtcatacttggtgcatgtttagtataattgtttcatattgcatctgtttttgacgagcttctttgattttatatactgtataatgcag

Basic information

species Glycine max
transcript GLYMA16G05450.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G05450.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os06g10810.1 (Oryza sativa), 5'ss of exon 4
TGGTGGATATATTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtcatacttggtgca-tg-tttagtataattgtttcatattgcatctgtttttgacgagcttctttgat--tttatatactgta-taatgcag--------
|||||| || ||||| |||||  | ||||| ||||| ||||| || || |||||||| |||||||| ||||||||||| || || || ||||| |||||||||||| |  |||||  | || || | | |||| | ||  |  |  ||| | || ||||||  || ||  |||||     |   | |  | | ||| |         
TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCAGATAATCTAGTCTCTTTCCTGAACAATGCCAAGGGTGCTACAGTGGGTGATgtgagtttattacttattacaatgctctggtattaatgcattgtggtgc-tttgcttttga--agttttgttgatgagcaactgattacagttatgtatttctgtag

upper sequence: GLYMA16G05450.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os04g37600.1 (Oryza sativa), 5'ss of exon 4
TGGTGGATATATTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtcatacttggtgcat-gtttagtataattgtttcatattgcatctgtttttgacgagcttctttgattttatatactgtataatgcag
 ||||| || ||||| || ||  | |||||||| || || || ||||| || |||||||| ||||| || |||||||| || || ||||||||||| ||||| ||| |  || |      |   | |  | |||    ||  | ||| || | || ||        |  |||  |||| |               
AGGTGGTTACATTGCAGGGGTGTTCTGTGCAATAGTTTCACACCCTGCGGACAATCTTGTGTCTTTCCTCAACAATGCCAAGGGCGCAACAGTTGGCGATgtaagttttgtaatcaccataccatcttctgtaacgtgtt--tgttggatttattatt------tcttgttgcatttacag--------------

upper sequence: GLYMA16G05450.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G152827_T01 (Zea mays), 5'ss of exon 4
TGGTGGATATATTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgt-catacttggtgcatgtttagtataattgttt-catattgcatctgtttttgacgagcttctttgattttatatactgtataatgcag
|||||| || ||||| |||||  | ||||| ||||| ||||| || ||||| || ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||  |  || |||| | ||||  |   | |  | | | | | ||| | ||  |    |   | |   |    ||  |||| | |    |||||
TGGTGGTTACATTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatatattcttgct-catgcatcaaacatgtatctacgtcttgtacctactagctattggttatatattgttgctatattct----tgcag

upper sequence: GLYMA16G05450.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G060630_T01 (Zea mays), 5'ss of exon 4
TGGTGGATATATTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtcatacttggtgcatgtttagtataattg---tttcatattgcatctgtttttgacgagcttctttgattttatatactgtataatgcag
|||||| || |||||||||||  | ||||| ||||| ||||| || || ||||| ||||| ||||| ||||||||||| || |  || || ||||| ||||| ||| | ||| |   ||| | |  || |    ||   |||| | |||    |  | ||    |  | | |||    || ||  | || |      
TGGTGGTTACATTGCTGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCCGATAACCTTGTGTCTTTCCTGAACAATGCCAAGGATGCTACTGTTGGCGATgtaagtat-atattct-tgcttttgcagcaggcatgcattttcttgttgtgcttactatttgtta--tacattgtcgctacatttt-tacag-----

upper sequence: GLYMA16G05450.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G015401_T01 (Zea mays), 5'ss of exon 4
TGGTGGATATATTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgt-catacttggtgcatgtttagtataattgttt-catattgcatctgtttttgacgagcttctttgattttatatactgtataatgcag
|||||| ||  |||| |||||  | ||||| ||||| ||||| || ||||| || ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||  |  || |||| | ||||  |   | |  | |   | | ||| | ||  |    |   | |   |    ||  |||| | |    |||||
TGGTGGTTACGTTGCCGGTGTCTTCTGTGCTATTGTTTCTCACCCGGCTGACAACCTTGTGTCTTTCCTGAACAATGCCAAGGGAGCTACAGTGGGAGATgtaagcatatattcttgct-catgcatcaaacatgtatcgacgtcttgtacctactagctattggttatatattgttgctatattct----tgcag

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|151407494|gb|EV277309.1|EV277309
EST:     GCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: GCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|9439983|gb|BE440494.1|BE440494
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|7591542|gb|AW707273.1|AW707273
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAGAGGAGCCACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGGCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|192324693|gb|FK018759.1|FK018759
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|19938613|gb|BQ081803.1|BQ081803
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|10237660|gb|BE806548.1|BE806548
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|23052981|gb|BU577472.1|BU577472
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|21888708|gb|BQ741921.1|BQ741921
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|13481245|gb|BG510588.1|BG510588
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|7588312|gb|AW704110.1|AW704110
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCANAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTTCACTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|22526003|gb|BU084814.1|BU084814
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|23728600|gb|BU762362.1|BU762362
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
EST: gi|17022287|gb|BM093321.1|BM093321
EST:     ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGAT                         GCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC
genomic: ATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtca ... tataatgcagGCGGTGAAGAAGCTTGGCCTGTGGGGTCTCTTTACCCGTGGTCTTCCCCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGATATATTGCTGGTGTACTTTGTGCAATTGTGTCTCATCCTGCTGATAATCTTGTCTCTTTTCTGAACAATGCAAAAGGAGCAACAGTTGGTGATgtgagtgtcatacttggtgcatgtttagtataattgtttcatattgcatctgtttttgacgagcttctttgattttatatactgtataatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA