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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTTGGCTGCTGCTCAAGCACGACTATGGAATGTGAGGGAAGAGAGAGACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAGgtttgaggttctatttttcatggctgcgtattgttaaagcaatgttcctgaatagtgttactctcagcatcctgttgtctaaaattttgatttgaccttgattgacag

Basic information

species Glycine max
transcript GLYMA20G38530.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38530.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os05g06980.1 (Oryza sativa), 5'ss of exon 12
TACTTTGGCTGCTGCTCAAGCACGACTATGGAATGTGAGGGAAGAGAGAGACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAGgtttgaggttctatttttcatggctgcgtattgttaaagcaatgttcctgaatagt-gttactctcagcatcctgttgtctaaaattttgatttgaccttgattgacag
  |  |   |||||||   | ||| ||   |||    ||||||||||| ||||| ||||| |||||||||||||| ||  |     |  | || | ||||||     | | |     ||||   |  | |    |     |   ||||   ||  | |||||||  |    | |||| |      |||  || | | |||         
ATCACTAAATGCTGCTGCTGGACGCCTCAAGAAAACCAGGGAAGAGAGGGACCAATTTGATGAAGCAAACAATCAAATTATATTTAAATTAAAAACAAAGgt-----gcttttcccatcatacttctgaagaacttgttta---ttcccatatgtttgttactcaaaatgacttgtttttc----tttccatatcaacttag-------

upper sequence: GLYMA20G38530.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G030235_T05 (Zea mays), 5'ss of exon 4
TACTTTGGCTGCTGCTCAAGCACGACTATGGAATGTGAGGGAAGAGAGAGACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAGgtttgaggttctatttttcatggctgc----gtattgttaaagcaatgttcct-gaatagtgt--tactctcagcatcctgttgtctaaaattttgatttgaccttgattgacag--------------------------------------------------------------
  |  |   |||||||   | ||| ||     |    ||||||||||| ||||| ||||| |||||||||||||| ||  |      | |||| | ||||||    |  | || ||||  ||| ||     || |  ||  |  ||| |||   |||  ||||  |||| ||    |||  |  |        |  | |||       | ||                                                                 
ATCACTAAATGCTGCTGCTGGACGGCTCAAACAAACTAGGGAAGAGAGGGACCAATTTGACGAAGCAAACAATCAAATCATATTTAGCTTGAAAAAAAAGgtgctggtgtttactttttgtggttgatccagtctaatttgaataatattctaagaactgtgtattactgtctttctcccatgatacttttcatcaacttgtggcctgtcgattctttcccatcatatttgttgctcaagatggtgcttgttgcatttcatttccaaatctatttag

upper sequence: GLYMA20G38530.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G102196_T01 (Zea mays), 5'ss of exon 8
TACTTTGGCTGCTGCTCAAGCACGACTATGGAATGTGAGGGAAGAGAGAGACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAGg----tttgaggttctatttttcatggctgcgtattgttaaagcaatgttc---ctgaatagtgtt-actctcagcatcc----tgttgtctaaaattttgatttgac--cttgattgacag--
| |  ||  |||||||      ||||||  | |    || |||||||| ||||||||| | |||||||||||||||||  |        |  |   |||||    |      ||||  || ||  |  |  || ||| |   ||  | ||      ||  | |||| | | || |  | |    ||||| ||| | |  |  ||||    ||  ||  |||   
TTCACTGAATGCTGCTATTTGTCGACTAAAGCAGACAAGAGAAGAGAGGGACCAGTTTCATGAAGCAAACAATCAGATGATATTTACTTTACAAGCAAAGgtggctacacttttctgattatccagtttcagttttgatcctgctgtatttgatgggatcaatgtttattatctgttttcaatatgttgactagattgatattttgttttctgcatcaacacag

upper sequence: GLYMA20G38530.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G102196_T02 (Zea mays), 5'ss of exon 8
TACTTTGGCTGCTGCTCAAGCACGACTATGGAATGTGAGGGAAGAGAGAGACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAGg----tttgaggttctatttttcatggctgcgtattgttaaagcaatgttcc---tgaatagtgtt-actctcagcatcc----tgttgtctaaaattttgatttgaccttg--attgacag-----
| |  ||  |||||||      ||||||  | |    || |||||||| ||||||||| | |||||||||||||||||  |        |  |   |||||    |      ||||  || ||  |  |  || ||| |   ||  | ||      ||  | |||| | | || |  | |    ||||| ||| | |  |  ||||   |    ||  |||      
TTCACTGAATGCTGCTATTTGTCGACTAAAGCAGACAAGAGAAGAGAGGGACCAGTTTCATGAAGCAAACAATCAGATGATATTTACTTTACAAGCAAAGgtggctacacttttctgattatccagtttcagttttgatcctgctgtatttgatgggatcaatgtttattatctgttttcaatatgttgactagattgatattttgttttctgcatcaacacaggag

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|6951428|gb|AW423496.1|AW423496
EST:     ACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAG                         GAAGATGAACTTTCAAAATCAGTTAGCTCATGTAGGGTTGAAGCAGATGTT
genomic: ACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAGgtttgaggtt ... tgattgacagGAAGATGAACTTTCAAAATCAGTTAGCTCATGTAGGGTTGAAGCAGATGTT
EST: gi|207762194|gb|GD731109.1|GD731109
EST:     ACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAG                         GAAGATGAACTTTCAAAATCAGTTAGCTCATGTAGGGTTGAAGCAGATGTT
genomic: ACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAGgtttgaggtt ... tgattgacagGAAGATGAACTTTCAAAATCAGTTAGCTCATGTAGGGTTGAAGCAGATGTT
EST: gi|151410338|gb|EV280153.1|EV280153
EST:     ACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAG                         GAAGATGAACTTTCAAAATCAGTTAGCTCATGTAGGGTTGAAGCAGATGTC
genomic: ACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAGgtttgaggtt ... tgattgacagGAAGATGAACTTTCAAAATCAGTTAGCTCATGTAGGGTTGAAGCAGATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTTTGGCTGCTGCTCAAGCACGACTATGGAATGTGAGGGAAGAGAGAGACCAGTTTGAAGAAGCAAACAATCAGATAGTTGAACACCTGAAGATAAAGgtttgaggttctatttttcatggctgcgtattgttaaagcaatgttcctgaatagtgttactctcagcatcctgttgtctaaaattttgatttgaccttgattgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA