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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAGATCTTGGTTATGCTCCTGAGCTTGGAAACTATGCAGAATATAGTGGTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGATgtaatcaattcttatctcaaacattatcgtcggtattgcaaaaaattcaagtcccaaattgactagagataaggcaaagatagaatatataaatagggga...

Basic information

species Glycine max
transcript GLYMA15G42140.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G42140.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 11
AGGAGATCTTGGTTATGCTCCTGAGCTTGGAAACTATGCAGAATATAGTGGTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGATgtaatcaattcttatctcaaacattatcgtcggtattgcaaaaaattcaagtcccaaattgactagagataaggcaaagatagaatatataaatagggga-
 || ||||| ||||||||| |||||||||| ||||||||||| |||||||| ||||| || ||||| || || ||||||||||| ||||| || ||||||||||   | || | | |   |   ||  |  |  |    |    | |  |    | ||||   |     ||||       |    |   | ||||      
TGGTGATCTCGGTTATGCTTCTGAGCTTGGGAACTATGCAGAGTATAGTGGAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaag-gactcatctgtaccatgctagagatgaaacattattttaattgatatgctaatttgtttattttaagtagtttttttccttattcaatatatcgc
















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|14991230|gb|BI316903.1|BI316903
EST:     GTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGAT                         TGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGA
genomic: GTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGATgtaatcaatt ... ctctttgcagTGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGA
EST: gi|7924163|gb|AW830189.1|AW830189
EST:     GTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGAT                         TGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGA
genomic: GTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGATgtaatcaatt ... ctctttgcagTGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGA
EST: gi|6502280|gb|AW203653.1|AW203653
EST:     GTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGAT                         TGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGA
genomic: GTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGATgtaatcaatt ... ctctttgcagTGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGA
EST: gi|6726078|gb|AW310477.1|AW310477
EST:     TGCACCC-AGGNAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGAT                         TGTGCAACTTCAAATCCTGATGGCC-AAAGCGAGCCCCTTGTGGTAGGTGG
genomic: TGCACCCAAGG-AAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGATgtaatcaatt ... ctctttgcagTGTGCAACTTCAAATCCTGATGGCCAAAAGCGAG-CCCTTGTGGTAGGTGG
EST: gi|192330363|gb|FK021164.1|FK021164
EST:     GTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGAT                         TGTGTAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGA
genomic: GTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGATgtaatcaatt ... ctctttgcagTGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGA
EST: gi|10253168|gb|BE820934.1|BE820934
EST:     GTGCACCCAAGGAAGATGANNNCTTGCAGTATGCCAGAGTAGTGATTGAT                         TGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTNNN
genomic: GTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGATgtaatcaatt ... ctctttgcagTGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAGATCTTGGTTATGCTCCTGAGCTTGGAAACTATGCAGAATATAGTGGTGCACCCAAGGAAGATGAGGTCTTGCAGTATGCCAGAGTAGTGATTGATgtaatcaattcttatctcaaacattatcgtcggtattgcaaaaaattcaagtcccaaattgactagagataaggcaaagatagaatatataaatagggga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaaaa