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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaaatttaaactcaatgactctgacttttttttaatcattgtgttctagttttactgttggtactgaaatgtgattttttttgtactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTTGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC

Basic information

species Glycine max
transcript GLYMA20G30430.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9
gtttgaaatttaaact-caatgac-tctgacttttttttaatcattgtgttctagttttactgttggtactgaaatgtgattttttttgtactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTTGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC
|| |||| | | |||| | ||||   |    |   ||||  |||||   |||    ||| ||           |||   |||| |||       ||||||| ||||||||||| |||||||| |||||| |||| |||||||| || || |||||||| |||| ||| || ||||| ||  |||| || ||||||||||
gtctgaactctgaactgccatgatacccctgtgccttttcctcattcaattcc--cttttct-----------aattacatttctttc------tgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC

upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
---------gtttgaaatttaa--actcaatgactctgacttttttttaatcattgtgttctagttttactgttggtactg----aaatgtgattttttttgtactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTTGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC
          ||      ||||  | || |  |   | || ||    |  ||| | | ||    |  | ||| |  | ||     |  |   |      |     | |||||||||||||||| || ||||| || ||||||||||| |||||||| ||||||||| |||| ||||  || || ||||||||  | || || |||||||| |
gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagtttttttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC

upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgaaatttaaactcaatgactctgacttt---tttttaatcattgtgttctagttttactgttggtactgaaatgtgattttttttgtactg-tgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTTGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC
    | ||   |  |   ||  |  || |||     | |  | ||||| ||     | |||        |    ||   ||   ||||| | ||  |  ||||||| ||||||||||||||||| |||||||||||||||||||| || || |||||||| ||||||||||||||||| ||| | || |||||||| ||  
----gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtctatttgttatctaatccaaaataacaagaacatttttttgctactacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT

upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------------------------gtttgaaatttaaactcaatgactctgacttttt--tttaatcattgtgttctagttttactgttggtactgaaatgtgatttt----ttttgtactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTTGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC
                                             |||   ||  ||   |||   |   |        |||||   ||||  || | ||| |||| |   | ||||   | |   |    ||   | || |||||||||| ||||| || |||||||||| |||||||||||||||||| ||||| ||  | || ||||  ||||| ||||||||| | || |||||||||||||
gtcatttaacatatcctttatatttattttaatgctgcattggccttgtttttgtaatgtaattttttaaaaaaaaaagtttaaat-ttgtactccattttaactgctaacaatgaatacttaccataagcttcctttctctgtagAACCATATGAGCGAAATGTTTGCTTTCCATGCAACCATGATGTCCAATACTCTCAGTACTTCAATAGTTGTTTTCACTAGAACTGGTTTCATGGCTATCC

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|17022372|gb|BM093406.1|BM093406
EST:     CCACTATACCTGGTGGTCAAATGCCACCAAATATTGGTCAAGTATTCAAG                         AACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAAT
genomic: CCACTATACCTGGTGGTCAAATGCCACCAAATATTGGTCAAGTATTCAAGgtttgaaatt ... tactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAAT
EST: gi|10234302|gb|BE803190.1|BE803190
EST:     CCACTATACCTGGTGGTCAAATGCCACCAAATATTGGTCAAGTATTCAAG                         AACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACC
genomic: CCACTATACCTGGTGGTCAAATGCCACCAAATATTGGTCAAGTATTCAAGgtttgaaatt ... tactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACC
EST: gi|193513187|gb|FK469643.1|FK469643
EST:     AAATGCCACCAAATATTGGTCAAGTATTCAAG                         AACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACC
genomic: AAATGCCACCAAATATTGGTCAAGTATTCAAGgtttgaaatt ... tactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACC
EST: gi|192328427|gb|FK020715.1|FK020715
EST:     CCACTATACCTGGTGGTCAAATGCCACCAAATATTGGTCAAGTATTCAAG                         AACCACCTGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACC
genomic: CCACTATACCTGGTGGTCAAATGCCACCAAATATTGGTCAAGTATTCAAGgtttgaaatt ... tactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgttctagttttactgttggtactgaaatgtgattttttttgtactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTTGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC
                                    ttttttttgt  CT-rich tract
                            aaatgtgatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaaatttaaactcaatgactctgacttttttttaatcattgtgttctagttttactgttggtactgaaatgtgattttttttgtactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTTGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA