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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtttttctctaaattttttgaaatcttgttagtaatattatttgttgagatacatattacttactatttgcaaatgcattttttaaaatatattcttgcttctttcag

Basic information

species Glycine max
transcript GLYMA06G44340.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM5G816609_T01 (Zea mays), 5'ss of exon 2
GGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtttttctctaaatt--ttttgaaatcttgttagtaatattatttgttgagatacatattacttactatttgcaaatgcattttttaaaatatattcttgcttctttcag
 ||  ||||    || ||||| |  ||||| ||| |    ||  | ||||| |||||  ||||| | |||||||||||||||||||||||||| ||  |||||       |   | |||  |  | |||   |||  | | |     | ||  |    ||  ||| |  ||   |||| ||                                    
TGCTATTCTCATGGAGTATATTGGCAAAGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggactagtgcttgtaatctagtcttgctgtctcataacttggtgttttgttccttatcaatactctttttaattttcag-----------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G155384_T03 (Zea mays), 5'ss of exon 16
GGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtttttctctaaatt---ttttgaaatcttgttagt-aatattatttgttgagatacatattacttactatttgcaaatgcattttttaaaatatattcttgcttctttcag
 ||  ||||    || ||||| |  || || ||| |    ||  | ||||| |||||  ||||| | |||||||||||||||||||||||||| ||  |||||     |  | ||   ||||   | ||     ||  | | |   | || |||  | |   |  || |  ||   |||| ||                                    
TGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaactagtgcttataattgtgtcttactgcctcataatttggtgttgttttgttaatca-gtactgtttctaattttcag-----------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 16
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 5'ss of exon 14
GGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtttttctctaaattttttgaaatcttgttagtaatattat-ttgttgagatacatat-tacttactatttgcaaatgcattttttaaaatatattcttgcttctttcag
 || |||||    |  ||||| || || || ||  | ||  || | |||||||| ||||||||| | || ||||||||||| |||||||| ||||| ||||||      | || |||   ||   |    |  |      ||| || | |||  |||| |   |  | || ||| |||| | |                                  
TGCCCTTCTTTCAGGTTATATTGACAATGAGGATTCATCTGTCCGAATTGGTGCTATTATGGGTCTCGGGATTGCATATGCGGGTTCCCAAAATGATCAGgtgaatacatgttatcttc-ttacctatggtgctaagttgaatgttctgttgacgagacaataacatgctcactgtttggatag---------------------------------

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|193522231|gb|FK482104.1|FK482104
EST:     GTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAG                         TTACGGGAGAAATTGACAGGTGTACTGAACGTATTCTAAAGCTTCACTTGA
genomic: GTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtt ... cttctttcagTTACGGGAGAAATTGACAGGTGTACTGAACG-ATTCTAAAGCTTCACTTGA
EST: gi|193700466|gb|FK639057.1|FK639057
EST:     AATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAG                         TTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGAG
genomic: AATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtt ... cttctttcagTTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGAG
EST: gi|208298033|gb|GE093248.1|GE093248
EST:     GTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAG                         TTACGGGAGAAATTGACAGGTGTACTGAACGGTTCTAAAGCTTCACTTGAG
genomic: GTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtt ... cttctttcagTTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGAG
EST: gi|193344460|gb|FK311212.1|FK311212
EST:     GCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAG                         TTACGGGAGAAATTGACAGGTGTACTGGACGATTCTAAAGCTTCACTTGAG
genomic: GCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtt ... cttctttcagTTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGAG
EST: gi|193426783|gb|FK392568.1|FK392568
EST:     TGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAAGCAG                         TTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGA
genomic: TGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATG-AGCAGgtgttctgtt ... cttctttcagTTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGA
EST: gi|193340253|gb|FK307874.1|FK307874
EST:     GCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAG                         TTACGGGAGAAATTGACAGGTGTACTGGACGATTCTAAAGCTTCACTTGAG
genomic: GCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtt ... cttctttcagTTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGAG
EST: gi|193493116|gb|FK460902.1|FK460902
EST:     GTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAG                         TTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGAG
genomic: GTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtt ... cttctttcagTTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGAG
EST: gi|193481819|gb|FK446938.1|FK446938
EST:     GTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAG                         TTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGAG
genomic: GTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtt ... cttctttcagTTACGGGAGAAATTGACAGGTGTACTGAACGATTCTAAAGCTTCACTTGAG
EST: gi|208067895|gb|GD861405.1|GD861405
EST:     GCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAAGACAG                         TTACGGGAGAAATT
genomic: GCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGA-G-CAGgtgttctgtt ... cttctttcagTTACGGGAGAAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtttttctctaaattttttgaaatcttgttagtaatattatttgttgagatacatattacttactatttgcaaatgcattttttaaaatatattcttgcttctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG