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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attagtcattgtacaatttattaatatgattgtgatgtatatttaagttattttaatatgttcaatttttaactggtagttcttcaattttctgtgacagTTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG

Basic information

species Glycine max
transcript GLYMA06G15180.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15180.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 4
attagtcattgtacaatttattaatatgattgtgatgtatatttaagttattttaatatgttcaatttttaactggtagttcttcaattttctgtgacagTTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG
    || ||| |  | | |  |||  | |    |||  ||   | ||||    ||      ||   | ||   || ||  |   |   ||||| |  ||| | || ||||| || ||||| || ||||||||||| ||||||||||||||||||||||||
----gtaattatttactctcataaagtaa----gatacatgcctgagtt----ta------tccgctcttggttgataactagcc---tttctttttcagCTTTTAGATCTTCCAGGAATCATTGAGGGTGCTAAAGATGGAAAGGGTAGAGGAAGGCAG

upper sequence: GLYMA06G15180.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 4
attagtcattgtacaatttattaatatgattgtgatgtatatttaagt-tattttaatatgttcaatttttaactggtagttcttcaattttctgtgacagTTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG
  |   ||| || || || |  ||| | |     | || | | | ||  ||||| |   || | |||| ||||    | | | |||| ||        ||| |  | |||||||| || || ||||| |||||||| ||||||||||| |||||||| |||
-gtgaccat-gtgca-ttcagaaatctaa-----aagtttttctgagcatatttcatcttgattaattattaatatctggct-ttcattt--------cagCTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG

upper sequence: GLYMA06G15180.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 4
-attagtcattgtacaatttattaatatgattgtgatgtatatttaagttattttaatatgtt-caatttttaactggtagttcttcaattttctgtg-acagTTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG
 | |  |   |    | ||||  | |  |     ||  | || |||  | |||  |   || | | | |  |   |  ||  ||  |   | | |||   ||||| || ||||| || || ||||| ||||||||||| |||||||| ||||||||||| |||
gacttcttggtacttagttta--agtcaggaaacgacctgtaattat-tcattggacactgatgctaatactcttttttatgtccccttctatgtgtttgcagTTATTAGATCTTCCTGGTATTATTGAGGGTGCTAAAGATGGAAAAGGTAGAGGAAGACAG

upper sequence: GLYMA06G15180.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g01620.t01 (Vitis vinifera), 3'ss of exon 4
---------attagtcattgtacaatttattaatatgattgtgatgtatatttaagttattttaatatgttcaatttttaactggtagttcttcaattttctgtgacagTTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG
           |  ||| ||    |||  ||| |   ||||  | || |  || | || ||||  | | ||   ||||||| ||  ||||  |   |  |   || ||||||||||||||||| || ||||| |||||||||||||||||||| |||||||||||||||
gtgagccctggtgctcaatgcttgatt--ttacttctattgataggttttctttaattctttt--ttttttttttttttaattg--agtttctgtgtggt---tggcagTTGTTGGATCTCCCTGGTATTATTGAGGGTGCTAAGGATGGAAAAGGTAGAGGAAGGCAG

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|6454220|gb|AW184833.1|AW184833
EST:     CCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAG                         TTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGA
genomic: CCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAGgtatctctac ... tctgtgacagTTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGA
EST: gi|192294592|gb|FG986441.1|FG986441
EST:     CCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAG                         TTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGA
genomic: CCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAGgtatctctac ... tctgtgacagTTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGA
EST: gi|254325516|gb|GR838397.1|GR838397
EST:     CCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAG                         TTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGA
genomic: CCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAGgtatctctac ... tctgtgacagTTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttattttaatatgttcaatttttaactggtagttcttcaattttctgtgacagTTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG
                     ttttaac  putative branch site (score: 2)
                                  ttcttcaattttct  putative PPT
     ttttaatatgttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attagtcattgtacaatttattaatatgattgtgatgtatatttaagttattttaatatgttcaatttttaactggtagttcttcaattttctgtgacagTTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA