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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagtttggctgctcttagatgattagttatttgccacttagttctatcatacccgtaagattgactagtataattatttgctttcctctttcctcaacctccccctcttacag

Basic information

species Glycine max
transcript GLYMA15G15960.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G15960.2 (Glycine max), 5'ss of exon 15
lower sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 15
GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgta---tccaagtttggctgctc----ttagatgattagttatttgccacttagttctatcatacccgtaagattgactagtataattatttgctttcctctttcctcaacctccccctcttacag
| || ||||| ||| ||||||| ||||| ||||||||||||||||| || || |||   || || || || ||||||||||   |   | ||      | |       ||| ||  |  ||  || |||  |||      |  ||  ||  ||       ||| | |   | | |                             
GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttcatttgaatcacgcaggcaccgataataggagataagcaactctgtttcga-gtctccacaatgtttttcctcata-tgagaggttcttgaga------------------------

upper sequence: GLYMA15G15960.2 (Glycine max), 5'ss of exon 15
lower sequence: PP1S169_73V6.1 (Physcomitrella patens), 5'ss of exon 14
GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagtttggctgctcttagatgattagttatttgccacttagttctatcatacccgtaagattgactagtataattatttgctttcctctttcctcaacctccccctcttacag
|||| ||||| || |||||||| ||||| |  |||||||| || ||||| |||||| | || |||||||| ||||||||||| | |       |   ||| |||   ||  ||| |   |   |  |  || ||||  |         | || | | || |    || || |    || ||                
GTGATAATGGAAGTATGTGGTTTTGGGACTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc---attttcctttgatatatatatatatat-atacatatacat-atacatgctttccgtgcgaggagacttttggaattgccccacatctgaata--------------

upper sequence: GLYMA15G15960.2 (Glycine max), 5'ss of exon 15
lower sequence: PP1S402_49V6.1 (Physcomitrella patens), 5'ss of exon 15
GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagtttggctgct--cttagatgattagttatttgccacttagttctatcatacccgtaagattgactagtataattatttgctttcctctttcctcaacctccccctcttacag
|||| ||||| ||  ||||||| |||||||  || ||||| ||||| ||||||||| | || ||||| || ||||||||||||| |         |   |||  | ||||  || |  || |        | ||| |   ||  | | | ||  ||| |     | || |  | | |  |                   
GTGATAATGGAAGTTTGTGGTTTTGGGATTACAAAAGTGGGCATAACTTCCAGCAAGCGCAGACAATCGTGCAGCCTGgtatcctaccaccatcacctacttgcacgatttcttttaagctaaacttgcatgtcaca---gtttggtgggcttatattaggggatactatt-tatatggtgg-----------------

upper sequence: GLYMA15G15960.2 (Glycine max), 5'ss of exon 15
lower sequence: EFJ31158 (Selaginella moellendorffii), 5'ss of exon 17
GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagtttggctgctcttagatgattagttatttgccacttagttctatcatacccgtaagattgactagtataattatttgctttcctctttcctcaacctccccctcttacag
|||| ||||| ||||| |||||||||||||||| ||| || ||||| ||||||||| | ||||| || || ||||| ||||  ||  || |   |    | |   |   |||   |  | |||  |  |  ||                                                                
GTGATAATGGAAGCATCTGGTTCTGGGATTGGACGAGCGGCCATAACTTCCAGCAAACTCAAACCATCGTTCAGCCAGgtacgcattttggtggggaagtggtcca--ggttgcgtaactcttgctcatggcag---------------------------------------------------------------

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|193446770|gb|FK411733.1|FK411733
EST:     TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG                         GTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
genomic: TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagt ... cctcttacagGTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
EST: gi|6070929|gb|AW100316.1|AW100316
EST:     TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG                         GTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
genomic: TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagt ... cctcttacagGTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
EST: gi|254313964|gb|GR831593.1|GR831593
EST:     TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG                         GTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
genomic: TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagt ... cctcttacagGTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
EST: gi|254319813|gb|GR829217.1|GR829217
EST:     TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG                         GTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
genomic: TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagt ... cctcttacagGTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
EST: gi|21993683|gb|BQ785211.1|BQ785211
EST:     TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG                         GTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
genomic: TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagt ... cctcttacagGTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
EST: gi|37994708|gb|CF806333.1|CF806333
EST:     TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG                         GTTCCCTGGATAGTGAAGCTGGTATTTATGC
genomic: TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagt ... cctcttacagGTTCCCTGGATAGTGAAGCTGGTATTTATGC
EST: gi|193558888|gb|FK514511.1|FK514511
EST:     TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG                         GTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG
genomic: TTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagt ... cctcttacagGTTCCCTGGATAGTGAAGCTGGTATTTATGCTTGTACCTATGATCTTACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgtatccaagtttggctgctcttagatgattagttatttgccacttagttctatcatacccgtaagattgactagtataattatttgctttcctctttcctcaacctccccctcttacag

- - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - GGAAGA