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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAACTAGGTGTTACCTGGGATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctcttgtgtctctcattccataaccaaagttttgaacaacagtccaggaccacagttgccatcacaacatcaaggtttttgagtctcgtgacaa...

Basic information

species Glycine max
transcript GLYMA04G36600.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36600.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 2
AGAGAACTAGGTGTTACCTGGGATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctcttgtgtctctcattccataaccaaagttttga-acaacagtccaggacc-acagttgccatcacaacatcaaggtttttgagtctcgtgacaa---------------------------------------------------
|||||| | |||||||||||||||||||||||||| || || ||||| |||||||| || ||||| |||||||   |    |       | |  | | ||    ||       ||||   ||   |    |   ||   | |  ||| |    |  || |||| |  |   |                                                    
AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAAATTGGGGGTGGAAAGGAAAGgtaatttctcttctcaaataagcctaaaaaagcagcaccactacaaggatctttgttttattattcttaac-taacttgtgtggattggagtttaattgtagatgaacttcattcaagttgatttagttattgagagatttggctcttttcag

upper sequence: GLYMA04G36600.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ31567 (Selaginella moellendorffii), 5'ss of exon 2
AGAGAACTAGGTGTTACCTGGGATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctcttgtgtctctcattccataaccaaagttttgaacaacagtccaggaccacagttgccatcacaacatcaaggtttttgagtctcgtgacaa
| || | | |       |||||| |||||  | ||||| |||||||| || ||||||||||| |||||| |||||||||     ||   || |            ||| |  |||   |        || ||||    |   ||| || |   ||   ||  || || || 
AAAGGATTGGACACAGTCTGGGACGTGGAGCTCTACGGAGAATTGCTCAAGATTGGAGGCGGCAAAGAACGgtttgtcttgcaagttcttcgt------------gttct--acactgg--------caaagtt----tgttaacttcgatacttccaagcttcttggcag

upper sequence: GLYMA04G36600.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ38583 (Selaginella moellendorffii), 5'ss of exon 2
AGAGAACTAGGTGTTACCTGGGATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctcttgtgtctctcattccataaccaaagttttgaacaacagtccaggaccacagttgccatcacaacatcaaggtttttgagtctcgtgacaa
| || | | |       |||||| |||||  | ||||| |||||||| || ||||||||||| |||||| |||||||||     ||   || |            ||| | |||             || ||||  | | |  || || |   ||   ||| || || || 
AAAGGATTGGACACAGTCTGGGACGTGGAGCTCTACGGAGAATTGCTCAAGATTGGAGGCGGCAAAGAACGgtttgtcttgcaagttcttcgt------------gttctaaactgg----------caaagtt--cgtta--acttcgatacttccaagtttcttggcag

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|213615268|gb|DB963462.1|DB963462
EST:     GACGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
EST: gi|19271225|gb|BM887481.1|BM887481
EST:     GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
EST: gi|15204351|gb|BI427119.1|BI427119
EST:     GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
EST: gi|22522372|gb|BU081183.1|BU081183
EST:     GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
EST: gi|209718040|gb|BW671873.1|BW671873
EST:     GACGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
EST: gi|20811539|gb|BQ296017.1|BQ296017
EST:     GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
EST: gi|20813568|gb|BQ298046.1|BQ298046
EST:     GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
EST: gi|19269931|gb|BM886187.1|BM886187
EST:     GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
EST: gi|209704519|gb|BW680649.1|BW680649
EST:     GACGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTG
EST: gi|213600087|gb|DB970233.1|DB970233
EST:     GACGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
EST: gi|213597882|gb|DB958263.1|DB958263
EST:     GACGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCAGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG
EST: gi|22541489|gb|BU091332.1|BU091332
EST:     -ATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAG                         GATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACANG
genomic: GATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctct ... ttatgactagGATGACAGCATACTTTAACAAGGTGGGTTGGCCTGCGAATGCCCCAACAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAACTAGGTGTTACCTGGGATGTGGACTTGTACGGGGAATTGCTGAAAATTGGAGGCGGAAAAGAAAGgtttgtctcttgtgtctctcattccataaccaaagttttgaacaacagtccaggaccacagttgccatcacaacatcaaggtttttgagtctcgtgacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA