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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatttccatgtcctaaacctttctctatcttacagattcagttagatacttagatttcaatattttgaagtgatttgtttttcaactattatgaatttatttttagGCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTATTATTGGAGATGAATCATCCATTTCGGTATCAATTAGCCGTACCTCTTG

Basic information

species Glycine max
transcript GLYMA19G30460.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30460.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G26120.1 (Arabidopsis thaliana), 3'ss of exon 3
gttatttccatgtcctaaacctttctctatcttacagattcagttagatacttagatttcaatattttgaagtgatttgtttttcaactattatgaatttatttttagGCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTATTATTGGAGATGAATCATCCATTTCGGTATCAATTAGCCGTACCTCTTG
                             | ||   ||||   |     | ||   | | ||  |||| |    |     |  | ||  |  ||   |||  || |||| ||||||||||| || | || || | | |  ||| | |    |||||| |||||||||||||||||||||||||  ||    |    |||| | || ||
----------------------------gtttttgtgattttatcttggagttttctataaagcttttcattaaaaagaatggtgaataaaaatc--tttggttatagGATTTGAAGCTGGTGGACAAATCATTCCTTCCAATATCTGGCCTTGGTCCATTATTGGAGATGAATCATCCATTTATGTTGTTACAGACCGTTCTTCGTG
















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|193466669|gb|FK432090.1|FK432090
EST:     TAATCATGCTGGCGCAGGGGGACTGTGGGCTGAACTTGTTATCAATAGAG                         GCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTA
genomic: TAATCATGCTGGCGCAGGGGGACTGTGGGCTGAACTTGTTATCAATAGAGgttatttcca ... ttatttttagGCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTA
EST: gi|213591414|gb|DB955734.1|DB955734
EST:     TAATCATGCTGGCGCAGGGGGACTGTGGGCTGAACTTGTTATCAATAGAG                         GCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTA
genomic: TAATCATGCTGGCGCAGGGGGACTGTGGGCTGAACTTGTTATCAATAGAGgttatttcca ... ttatttttagGCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTA
EST: gi|193491629|gb|FK454249.1|FK454249
EST:     TAATCATGCTGGCGCAGGGGGACTGTGGGCTGAACTTGTTATCAATAGAG                         GCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTA
genomic: TAATCATGCTGGCGCAGGGGGACTGTGGGCTGAACTTGTTATCAATAGAGgttatttcca ... ttatttttagGCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTA
EST: gi|213617613|gb|DB969325.1|DB969325
EST:     TAATCATGCTGGCGCAGGGGGACTGTGGGCTGAACTTGTTATCAATAGAG                         GCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTA
genomic: TAATCATGCTGGCGCAGGGGGACTGTGGGCTGAACTTGTTATCAATAGAGgttatttcca ... ttatttttagGCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttcaatattttgaagtgatttgtttttcaactattatgaatttatttttagGCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTATTATTGGAGATGAATCATCCATTTCGGTATCAATTAGCCGTACCTCTTG
                                            tttattttt  CT-rich tract
                   tgatttgtttttcaac  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatttccatgtcctaaacctttctctatcttacagattcagttagatacttagatttcaatattttgaagtgatttgtttttcaactattatgaatttatttttagGCTTTGAAGCTGGAGGCCCAAACAATGCCTTAAATGTTTATAATTGGTCTATTATTGGAGATGAATCATCCATTTCGGTATCAATTAGCCGTACCTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG