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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCATGGATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgttgtaatgtgtcttttcattcttttatctatatcaatttatatgatccattttaaaatcaacttatgcatctcaacttctgaaaaaattaga...

Basic information

species Glycine max
transcript GLYMA01G27840.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G27840.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g04920.1 (Oryza sativa), 5'ss of exon 10
TCTCATGGATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgttgtaatgtgtcttttcattcttttatctatatcaatttatatgatccattttaaaatcaacttatgcatctcaacttctgaaaaaattaga-
  | ||||||||||| |||| || | ||||||| ||||| ||||||||||| ||||||| || |  | |   ||  |||  |||| | |   |||||||  ||| | |  |    ||  |  |   | |   || |   |  ||  ||   |||  | 
GGTAATGGATAGGCTGCCTGGAGTAAGAATTGCATTTATTGGAGATGGACCATACAGgt-atatcatatgtggttccttgccattttatatactatatctttttttttcctaagcttccagtttgtcatgaacagcggcagctcaaaatttattgcat
















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|151397927|gb|EV267800.1|EV267800
EST:     GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAG                         AGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
genomic: GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgtt ... acctgaacagAGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
EST: gi|8669562|gb|BE190669.1|BE190669
EST:     GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAG                         AGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
genomic: GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgtt ... acctgaacagAGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
EST: gi|254336464|gb|GR842643.1|GR842643
EST:     GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAG                         AGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
genomic: GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgtt ... acctgaacagAGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
EST: gi|15663309|gb|BI700680.1|BI700680
EST:     GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAG                         AGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
genomic: GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgtt ... acctgaacagAGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
EST: gi|298196742|gb|HO041485.1|HO041485
EST:     GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAG                         AGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
genomic: GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgtt ... acctgaacagAGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
EST: gi|254336465|gb|GR842644.1|GR842644
EST:     GCACGAATTGCCTTTATCGGAGATGGACCTTACAG                         AGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
genomic: GCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgtt ... acctgaacagAGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
EST: gi|8669561|gb|BE190668.1|BE190668
EST:     GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAG                         AGAGGAACTAGAG
genomic: GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgtt ... acctgaacagAGAGGAACTAGAG
EST: gi|254334106|gb|GR849024.1|GR849024
EST:     GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAG                         AGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTC
genomic: GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgtt ... acctgaacagAGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTC
EST: gi|21888687|gb|BQ741900.1|BQ741900
EST:     GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAG                         AGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT
genomic: GATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgtt ... acctgaacagAGAGGAACTAGAGAAAATGTTTGAAGGCATGCCAGCAGTGTTCACAGGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCATGGATAGGCTTCCTGAAGCACGAATTGCCTTTATCGGAGATGGACCTTACAGgtgatttgttgtaatgtgtcttttcattcttttatctatatcaatttatatgatccattttaaaatcaacttatgcatctcaacttctgaaaaaattaga

- - - - - - - -  CTGAAG
- - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaaaaa