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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtataatattgccttaaaacagttagtattgaaattagttcttttgtttttgttttcaaaacccagaattgattaaaatcttttcctttttcatacagaTGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTG

Basic information

species Glycine max
transcript GLYMA18G48370.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g10784.1 (Oryza sativa), 3'ss of exon 7
ggtataatattgccttaaaacagttagtattgaaattagttcttttg--tttttgttttcaaa-acccagaattgattaaaatct-tttcctttttcatacagaTGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTG
   ||  |  ||  |   || | ||| | ||| |     | |        || ||||||  |   |        | || || ||| ||| | ||   | ||||||||| | |||||||||||| | || || |||||| |||||||||| ||||||||  || 
--cattgt-ctgtttattaatatttatttttgcaccctctccaaagaaaattatgtttttgattgcttcatgacggttgaattctgttttcattccgacacagATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATTGTCCAGTT-

upper sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G79500.2 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------------------------------------ggtataatattgccttaaaacagttagtatt-gaaattagttcttttgtttttgttttcaaaacccagaattgattaa-----aatcttttcctttttcata--cagaTGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTG
                                                                                         | || ||||  ||     |||    ||| ||   |  |       ||||| || ||       | |||||| | |     | ||||||   |||| ||   ||||||||||||| || |||||||| ||||| ||||||||||||||||| ||||||||  || 
gtaagttatcatctccttttcaaatattgtgtccacggaatttagtattgtagatattctcaaatctcatgcaaatctcttggaattaaaaaaaattggattgctgaagtatacattagagggtgctaaaacaattttttttctctgcctttacaattgactgactgatactctttttggttttgattatcagATGATTTGATAGTAGATCCACGAAACTTCGAGTGGATGAGAGAAGCTAATTGTCCTGTT-

upper sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 7
--ggtataatattgccttaaaacagttagtattgaaattagttcttttgtttttgttttcaaaacccagaattgat-taaaatcttttcctttttcatacagaTGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTG
    |   |  | |   | |   |   | ||| || |||  | | ||  ||||| ||||    |  ||  |||||  | | || |   | ||  |  || ||||||| |||||||||||||||| ||||||||||||||||| ||||| |||||||| ||| 
catattggaagtagaggtcattgatgcattatagatatttttaccttcttttttttttttttcattca--attgaccttatatttgggctttgattttatagATGATCTGATTGTTGATCCACGCAACTTGGAGTGGATGAGGGAAGCTAATTGTCCTATT-

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|209696818|gb|BW680440.1|BW680440
EST:     GGAAATCCTAATGTGATGGTTTGTGAGAGAGGA-CAATGTTTGGATACAA                         TGATTTGATTGTTGA
genomic: GGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAGtgagttaata ... ttcatacagaTGATTTGATTGTTGA
EST: gi|208272394|gb|GE073208.1|GE073208
EST:     GGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAA                         TGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTG
genomic: GGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAGtgagttaata ... ttcatacagaTGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTG
EST: gi|192294788|gb|FG987477.1|FG987477
EST:     GGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAA                         TGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGGGAGAAGCCAATTG
genomic: GGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAGtgagttaata ... ttcatacagaTGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTG
EST: gi|193608170|gb|FK557083.1|FK557083
EST:     GGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAA                         TGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTG
genomic: GGAAATCCTAATGTGATGGTTTGTGAGAGAGGAACAATGTTTGGATACAGtgagttaata ... ttcatacagaTGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttgttttcaaaacccagaattgattaaaatcttttcctttttcatacagaTGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTG
                      aattgat  putative branch site (score: 4)
                                  tcttttcctttttcat  putative PPT
                      aattgattaaaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtataatattgccttaaaacagttagtattgaaattagttcttttgtttttgttttcaaaacccagaattgattaaaatcttttcctttttcatacagaTGATTTGATTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - -tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccagaa