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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcag

Basic information

species Glycine max
transcript GLYMA08G22140.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagtgga-tcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttact-cag
|| || || |||| ||| ||||| || ||||||||||||||||||||||| || |  |||||    || ||| | || ||||| ||||||||||  ||    |  ||  |      |  | |   | |||   ||  | | || |||   |    ||  | | ||  | |||
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttat--tgtct-ggtgttgaattcttgaac-taacatatttttcttgttgcag

upper sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagt-------ggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcag
|| |||||||||| ||||||||| || ||||||||||||||||||||| |||| | |||||||   || ||| | || ||||| || || ||||| ||         | ||||| ||    |  ||   |  ||||        ||||     | | |    ||  | ||    |||
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatct------gttaatttctctgactaacaaatagcttggtacag

upper sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G095348_T01 (Zea mays), 5'ss of exon 16
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaag-------tggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcag
|| |||||||||| ||||||||| || ||||||||| | |||||||||||||| | |||||||   || ||| | || ||||| || || ||||  |       |  | ||||| ||    |  ||   || ||||      | |     ||| ||   | |||  | || |  |||
GTCACTACAATGTATCATTTGGATCGCCCTATGTACCTATTGGGATATCTTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTTAAgtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataa--gcttgatacag

upper sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G086015_T01 (Zea mays), 5'ss of exon 1
--------GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagt-------ggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcag
        || |||||||||| ||||||||| || ||||||||| ||||||||||| |||| | |||||||   || ||| | || ||||| || || ||||| ||         | ||||| ||    |  ||   |  ||||        ||||     | | |    ||  | ||    |||
ACTTACAGGTCACTACAATGTATCATTTGGATCGCCCTATGTACCTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatct------gttaatttctctgactaacaaatagcttggtacag

upper sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 17
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagtggatcaatggtttgcattattcaaaatatctca-atgcagtaatcctga-ttatt-ttttaactgttttact-cag
||||||||||||||||| ||||| || |||||||| || || ||||||||||| | |||||||   || ||| | || ||||| ||||| |||||||  |       |  | | |  |||  |   ||| | |||  ||  |  ||  ||||      || | ||||| | |||
GTTACTACAATGTTTCACTTGGATCGGCCTATGTATTTATTAGGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAAgtaagcagcatg-cagcatacctacttctgatcttcttacatgatgtgtttttgggttatgacaacaatttttttattacag

upper sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 20
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttact-cag
|| |||||||||| |||| ||||||||||||||||||||||||| ||||| || |  ||||| | ||| |||||||| |||||||| ||||||||||  |||   |   |   || |||   || |      || |     |    || | | |  ||| | | | | |||
GTAACTACAATGTATCATCTGGACCGTCCTATGTACTTGTTGGGTTATCTCGCTAATCAAAGCAGGGTTTATTTGATTGACAAAGAGTTCAAgtaagcagatgttttactgttatgattgctaacaatgttttgtaacttactgacttctgtgtccactttatgattacag

upper sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 16
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattt----tttaactgttttactcag--------
|| || ||||||| |||||||||||| || ||||| ||||| || ||| |||||| ||||||   ||| || ||| | ||||||||||||||||| ||   |  ||  | ||  |||||  | |    |  ||   | |  | | |||   |    | |  |  |||| ||  |        
GTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAAgtacgttcctttata-tatgt-ttatttgagactgttttatcttgcatacataatttgctaacatatttccctttttcttgggaatgcag

upper sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 16
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcag----
|| || ||||||| |||||||||||| || ||||| ||||||||||||||||| || ||||||  ||| |  ||| | |||||||||||||||||||||  |  ||   |    ||||  ||   |  |   |  || | |      |  | ||   |||||||    |     
GTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAAgtaagtgcttagatttgtgtgtttatataattgagattgttctagaagtttctgatgctgttcccctgttttgtggatgcag

upper sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 16
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctga-----ttattttttaactgttttactcag----------
|| || |||||||||||||||||||| |||||||| |||||||||||||| || |  |||||   ||| ||| | || |||||||| ||||||| ||||||    |||     |              |   ||  ||| | || |     ||||| || |  || |||   |            
GTAACCACAATGTTTCATTTGGACCGGCCTATGTATTTGTTGGGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAAgtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcag

upper sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 16
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagtggatcaatggtttgcatt-----attcaaaatatctcaat----gcagtaatcctgattattttttaactgttttactcag
|| || || |||||||| |||||||| |||||||| ||||| |||||||||||||| ||||||   || ||| | || |||||||| || |||| || |       |   |||| |     | ||  | |   |   |    | | |    || | | | |||    | | |||  |||
GTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAAgtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcag

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|151411223|gb|EV281034.1|EV281034
EST:     CTATTTGATGGACAAAGAATTCAA                         TGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGT
genomic: CTATTTGATGGACAAAGAATTCAAgtaagtggat ... ttttactcagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA