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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTTATGAAATCAAGGAGGCATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAGgtaaatttcattttcctagtgcaagttgtgtatccactatggcttagcacagtttttgcctaatttgtaatttagtggtgtcatacatttgcatatcgagtctaattgaagcaagttggtgcttgctaactgttcttcaaaaaaaaatatcatcacactgcag

Basic information

species Glycine max
transcript GLYMA09G02030.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G02030.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os08g25799.1 (Oryza sativa), 5'ss of exon 5
GGGTTATGAAATCAAGGAGGCATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAGgtaaatttcattttcctagtgcaagttgtgtatccactatggcttagcacagtttttgcctaatttgtaatttagtggtgtcatacatttgcatatcgagtctaattgaagcaagttggtgcttgctaactgttcttcaaaaaaaaatatcatcacactgcag
| || | ||| | || || ||| | ||||||||||||||||||||| | ||||| |||   ||||||||||||| |    |||||       || | |  |   ||   ||   ||  ||||||    || |||   |  ||| || |    |||  | ||  |   ||   |  |                                                         
GAGTCAAGAACTAAAAGAAGCACTCAGAGCACAGATGGAAGTGCAACGAAAATTGCATGAACAAGTGGAGgtaagtaaagttttctcta---aaatggcatcagcatgttgaaataagacagttc--accaaatgcttctttttgttgcaa-atagttctgagttctgacattcct---------------------------------------------------------
















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|192317660|gb|FK011338.1|FK011338
EST:     CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAG                         GCGGAAAAGCACTTGCAGATTCGCCAGGATGCAGAGAGGAGATACATGGCG
genomic: CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAGgtaaatttca ... cacactgcagGCGGAAAAGCACTTGCAGATTCGCCAGGATGCAGAGAGGAGATACATGGCG
EST: gi|21600851|gb|BQ611182.1|BQ611182
EST:     CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAG                         GCGGAAAAGCACTTGCAGATTCGCCAGGATGCAGAGAGGAGATACATGGCG
genomic: CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAGgtaaatttca ... cacactgcagGCGGAAAAGCACTTGCAGATTCGCCAGGATGCAGAGAGGAGATACATGGCG
EST: gi|192325737|gb|FK015094.1|FK015094
EST:     CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAG                         GCGGAAAAGCACTTGCAGA
genomic: CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAGgtaaatttca ... cacactgcagGCGGAAAAGCACTTGCAGA
EST: gi|192323973|gb|FK015694.1|FK015694
EST:     CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAG                         GCGGAAAAGCACTTGCAGATTCGCCAGGATGCAGAGAGGAGATACATGGCG
genomic: CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAGgtaaatttca ... cacactgcagGCGGAAAAGCACTTGCAGATTCGCCAGGATGCAGAGAGGAGATACATGGCG
EST: gi|7147320|gb|AW509242.1|AW509242
EST:     CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCTAGTGGAG                         GCGGAACAGCACTTGCAGATTCTCCAGGATGCAGAGAGGAGATACATGGCG
genomic: CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAGgtaaatttca ... cacactgcagGCGGAAAAGCACTTGCAGATTCGCCAGGATGCAGAGAGGAGATACATGGCG
EST: gi|193471904|gb|FK437775.1|FK437775
EST:     CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAG                         GCGGAAAAGCACTTGCAGATTCGCCAGGATG
genomic: CATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAGgtaaatttca ... cacactgcagGCGGAAAAGCACTTGCAGATTCGCCAGGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTTATGAAATCAAGGAGGCATTGAGAGCACAGATGGAAGTGCAAAGTAAATTACATTTGCAAGTGGAGgtaaatttcattttcctagtgcaagttgtgtatccactatggcttagcacagtttttgcctaatttgtaatttagtggtgtcatacatttgcatatcgagtctaattgaagcaagttggtgcttgctaactgttcttcaaaaaaaaatatcatcacactgcag

- - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG