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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgtgactgcaacttcattatgtgaacttccacactgctgctaggaaacctgtcagcagtgtatgtcttctaaatctattcttatattgtactcttcagGTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATCCTGATCCTTGACACACACGCAGAAGTGTTTGTATGGATTGGTCAGTGTG

Basic information

species Glycine max
transcript GLYMA03G29280.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G180988_T02 (Zea mays), 3'ss of exon 17
gtgagtttgtgactgcaacttcattatgtgaacttccacact-gctgctaggaaacctgtcagcagtgta--tgtcttctaaatctattcttatattgtactcttcagGTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATCCTGATCCTTGACACACACGCAGAAGTGTTTGTATGGATTGGTCAGTGTG
                          |  |  ||   ||||| |||  |   | | || |     || |       |||    | | |  || ||| |   | ||||||||   ||| | | ||||||||||||||||||||||||||| || || ||  |||| ||||||||||| |  || || ||  | |||||||||||||| |
-------------------------gtcggtcctgttacacttgctcttcttagatctatattttgttttgcaaaattcagggtatctgattttatgggcttattcagGTAACTGAGATCTTCAACTTTTCCCAAGATGATTTGTTAACTGAAGACATGATGATACTTGACACACATGGTGAGGTTTTCATTTGGATTGGTCAGTGCG

upper sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G180988_T03 (Zea mays), 3'ss of exon 16
-gtgagtttgtgact--gcaacttcattatgtgaacttccacact-gctgctaggaaacctgtcagcagtgta--tgtcttctaaatctattcttatattgtactcttcagGTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATCCTGATCCTTGACACACACGCAGAAGTGTTTGTATGGATTGGTCAGTGTG
     |||  | ||   | |   |     |  |  ||   ||||| |||  |   | | || |     || |       |||    | | |  || ||| |   | ||||||||   ||| | | ||||||||||||||||||||||||||| || || ||  |||| ||||||||||| |  || || ||  | |||||           
tcatcgttgttaaccagggagactggaggtcggtcctgttacacttgctcttcttagatctatattttgttttgcaaaattcagggtatctgattttatgGGCTTATTCAGGTAACTGAGATCTTCAACTTTTCCCAAGATGATTTGTTAACTGAAGACATGATGATACTTGACACACATGGTGAGGTTTTCATTTGGAT-----------
















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|14126732|gb|BG791170.1|BG791170
EST:     CTCTTTTAATAGAGGAAAGTTACAG                         GTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATC
genomic: CTCTTTTAATAGAGGAAAGTTACAGgtgagtttgt ... tactcttcagGTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATC
EST: gi|8282536|gb|BE020027.1|BE020027
EST:     TTTAATAGAGGAAAGTTACAG                         GTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATC
genomic: TTTAATAGAGGAAAGTTACAGgtgagtttgt ... tactcttcagGTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATC
EST: gi|19935055|gb|BQ080085.1|BQ080085
EST:     CTCTTTTAATAGAGGAAAGTTACAG                         GTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATC
genomic: CTCTTTTAATAGAGGAAAGTTACAGgtgagtttgt ... tactcttcagGTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacctgtcagcagtgtatgtcttctaaatctattcttatattgtactcttcagGTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATCCTGATCCTTGACACACACGCAGAAGTGTTTGTATGGATTGGTCAGTGTG
                       ttctaaa  putative branch site (score: 2)
                                             tactcttc  putative PPT
                       ttctaaatctattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttgtgactgcaacttcattatgtgaacttccacactgctgctaggaaacctgtcagcagtgtatgtcttctaaatctattcttatattgtactcttcagGTAGAGGAGGTTTACAACTTTTCCCAAGATGATTTGTTAACAGAGGATATCCTGATCCTTGACACACACGCAGAAGTGTTTGTATGGATTGGTCAGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT