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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttctatttgcatctcactgcttacattgtaatgactcatgattggtggtcttgtgaaaacctgcaattttgtaggatgtctgctcaattaatttg...

Basic information

species Glycine max
transcript GLYMA07G04830.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G04830.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os01g52720.1 (Oryza sativa), 5'ss of exon 7
ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttctatttgcatctcactgct-tacattgtaatgactcatgattggtggtcttgtgaaaacctgcaattttgtaggatgtctgctcaattaatttg
|| ||||||||||| ||||| ||||||||||||||   |||||||||||| |||||||| ||||| ||  | ||  | | ||  ||| | || |  ||||||| ||| ||| | |  | |  | | |   || | ||||  |   |    | ||| | |     | | ||                              
ATATACACAGAGAACTGGGTGAATTCACCTGGACAACAGGAAGATAATTCGTGGCAAGCCTTTGTGTACTTACCCCAGGACAGATGGCAAATCATGAAGgtaatttcaattcgaagttgaaagatatggtttttgatgatacgacagcacttgtccttt-----ctttcag-----------------------------

upper sequence: GLYMA07G04830.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv09s0002g00680.t01 (Vitis vinifera), 5'ss of exon 6
ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttctatttgcatctcactgcttacat-tgtaatgactcatgattggtggtcttg-tgaaaacctgcaattttgtaggatgtctgctcaattaatttg--
|| || |||||||||||||| |||||||||| |||   ||||||||||||||||||||| ||||||| ||| ||  ||| ||||||||| ||||| |||| |||||||   |||  ||||  ||| |  | |||||||  |    ||    |  ||   ||  |   || | | |  ||  |     ||| |    |||||  
ATATATACAGAGAATTGGGTGAATTCACCTGCACAACAGGAAGATAATTCATGGCAAGCATTTGTTTTTGTACCAAAAGACAACTGGTATATTACAAAGgcaagttctg--tgctcctcaa-gctcatttgtgtaatgtgttgatataacagacctcactgtcatattggactatcatactactgtagctta-cagatttgaa
















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|192323993|gb|FK018684.1|FK018684
EST:     CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG                         ATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
genomic: CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttcta ... gattggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
EST: gi|298184473|gb|HO029686.1|HO029686
EST:     CATGGCAAGCTCTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG                         ATTCCTCTAGCTCGA
genomic: CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttcta ... gattggccagATTCCTCTAGCTCGA
EST: gi|298163373|gb|HO012106.1|HO012106
EST:     CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG                         ATTCCTCTAGCTCGA
genomic: CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttcta ... gattggccagATTCCTCTAGCTCGA
EST: gi|192318066|gb|FK007180.1|FK007180
EST:     CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG                         ATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
genomic: CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttcta ... gattggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
EST: gi|193701908|gb|FK639592.1|FK639592
EST:     CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG                         ATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGACGCA
genomic: CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttcta ... gattggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
EST: gi|192322997|gb|FK016728.1|FK016728
EST:     ATGGCAAGCTTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG                         ATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
genomic: ATGGCAAGC-TTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttcta ... gattggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
EST: gi|58014519|gb|CX701261.1|CX701261
EST:     CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG                         ATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
genomic: CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttcta ... gattggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
EST: gi|192318065|gb|FK007179.1|FK007179
EST:     CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG                         ATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
genomic: CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttcta ... gattggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
EST: gi|192325825|gb|FK018047.1|FK018047
EST:     CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG                         ATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
genomic: CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttcta ... gattggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAATGTTATAGATGCA
EST: gi|298177341|gb|HO027122.1|HO027122
EST:     CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG                         ATTCCTCTAGCTCGA
genomic: CATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttcta ... gattggccagATTCCTCTAGCTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAGgtaagttctatttgcatctcactgcttacattgtaatgactcatgattggtggtcttgtgaaaacctgcaattttgtaggatgtctgctcaattaatttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggtgg