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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGCGGAAGGGCGCTGGTGCTGGGAGGAAGCAATCGAGGAAAGCTGCTAAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCATgtatggattttcgtttcgttttgttaccaaatctgtttttttttttttttttgtgttctggcgattgaggttttggtgattgtttttgtttag

Basic information

species Glycine max
transcript GLYMA16G22060.4
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G22060.3 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os09g37910.3 (Oryza sativa), 5'ss of exon 2
TGAAGCGGAAGGGCGCTGGTGCTGGGAGGAAGCAATCGAGGAAAGCTGCTAAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCATgtatggattttcgtttcgttttgttaccaaatctgtttttttttttttttttgtgttctggcgattgaggtt--ttggtgattgtttttgtttag--
                    |||    |  || ||  ||  || || |  |||||||| |||||||||||||| || || ||||| |||||||| |||||||  |  | || | | |||   |||      |  ||  || |   ||       ||| |||   ||  | |   || | |  |||| || |||    
--------------------GCTCTCGGTGAGGAA--GACCAAGGCGGAGAAGGACCCGAACAAGCCGAAGAGGCCACCGAGCGCGTTCTTCGTGTTCATgt--gagtcttagatccgtgg-gtttttgtgttagtggttctccgttcgaagtggttttgggcgttctgatcgatttgggggtgttgttttttgcag

upper sequence: GLYMA16G22060.3 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G834758_T01 (Zea mays), 5'ss of exon 2
TGAAGCGGAAGGGCGCTGGTGCTGGGAGGAAGCAATCGAGGAAAG-CTGCTAAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCATg-----tatggattttcgtttcgttttgttaccaaatctgtttttttttttttttttgtgttctggcgatt-gaggttttggtgattgtttttgtttag--
   |||    |||||  |  ||  |      |||    ||| ||| | |  |||||||| |||||||| |||||  |||| |||||||||||||| ||||||     |  |  ||||    |||| |  ||       || | |  || ||| |   || |  |||  |||| ||  | ||  ||  ||  ||| | ||   
-AGAGCAAGGGGGCGGAGAAGCCCGCCAAGGGCAGGAAAGGGAAGGCCGGCAAGGACCCCAACAAGCCTAAGAGGGCTCCCAGCGCTTTCTTCGTGTTCATgtgagatgcgacttttttcgtcgtctctttttttttgctatatacttatttctggatgcga-ctgttgattcgatctatttttggatgcctttttatacag
















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|208283280|gb|GE087216.1|GE087216
EST:     AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCAT                         GTCCGAGTTCAGAGAGCAGTTCAAAGAAAGGAAGACATCCTAACAACA
genomic: AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCATgtatggattt ... ttttgtttagGTCCGAGTTCAGAGAGCAGTTCAA-GAA-GGA-G-CATCCTAACAACA
EST: gi|192297534|gb|FG989540.1|FG989540
EST:     AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCAT                         GTCCGAGTTCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGT
genomic: AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCATgtatggattt ... ttttgtttagGTCCGAGTTCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGT
EST: gi|15814123|gb|BI786398.1|BI786398
EST:     AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCAT                         GTCCGAGTTCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGT
genomic: AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCATgtatggattt ... ttttgtttagGTCCGAGTTCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGT
EST: gi|5058411|gb|AI736943.1|AI736943
EST:     AGGACCCTAACAAGCCGAAGAGACCTNCAAGCGCTTTTCTTCGTTTTCAT                         GTCCGAGTTCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGT
genomic: AGGACCCTAACAAGCCGAAGAGACCTCCAAGCGC-TTTCTTCGTTTTCATgtatggattt ... ttttgtttagGTCCGAGTTCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGT
EST: gi|10843286|gb|BF066593.1|BF066593
EST:     AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCAT                         GTCCGAGTTCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGT
genomic: AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCATgtatggattt ... ttttgtttagGTCCGAGTTCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGT
EST: gi|208239091|gb|GE037169.1|GE037169
EST:     AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCAT                         GTCCGAGTTCAGAGAGCAGTTCAAGAAGGAAGACATCCTAACAACA
genomic: AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCATgtatggattt ... ttttgtttagGTCCGAGTTCAGAGAGCAGTTCAAGAAGGA-G-CATCCTAACAACA
EST: gi|17401598|gb|BM178380.1|BM178380
EST:     AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCAT                         GTCCGAGTTCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGT
genomic: AAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCATgtatggattt ... ttttgtttagGTCCGAGTTCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGCGGAAGGGCGCTGGTGCTGGGAGGAAGCAATCGAGGAAAGCTGCTAAGGACCCTAACAAGCCGAAGAGACCTCCAAGCGCTTTCTTCGTTTTCATgtatggattttcgtttcgttttgttaccaaatctgtttttttttttttttttgtgttctggcgattgaggttttggtgattgtttttgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA