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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattatacgcccttctacacagtagtaatatttatgtaaattcttttgcactataagataaatatattcagcatttgaaaaacatttatcag

Basic information

species Glycine max
transcript GLYMA20G23080.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 8
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgt-tcattatacgcccttctacacagtagta--atatttatgtaaattcttttgcactataagataaatatattcagcatttgaaaaacatttatcag
|||||||||||||| |||||  |||| ||||||||||||||  |||| || ||||||||| | |||        ||  |||   | |||  | |  | | | |  | ||   | ||  |   | ||  | ||     | ||    |||        
AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaac-tgtttcctttgtggttcacag-------

upper sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 8
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattatacgcccttctacacagtagtaatatttatgtaaattcttttgcactataagataaata-tattcagcatttgaaaaacatttatcag
|||||||||||||| |||||  | || ||||||||||||||  ||||||| |||||||||   ||         ||     | | | |   | ||| |   | || ||    ||| |||  | || |  | | | | ||    |   ||  |||
AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtt---------tccctgaaattgaaccttgtatcttcttactatttggttattagaatattagtgctgaacctatgtcttatgcttcacag

upper sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 8
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcatt------atacgcccttctacacagtagtaatattta--tgtaaattcttttgcactataagataaata------tattcagcatttgaaa-aacatttatcag-----------------------------------------------------------
|||||||||||||| |||||  | || ||||||||||||||  ||||||| |||||||||   ||      | |||      || |   |  || | |||   | | | | | |     ||  || ||   |       || |     ||||||  || |     ||                                                            
AAAATCAAGAACCCGAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttgcctgaaacggatccttatatcttcttactgtttggctattactacgtcccttctcgaatatttgtggctcgctagttcatttttgaactaaaacgcgacaaataaaaaagaaaggagggagtagaatgttagtgctgaatctaattcttgtgcatcacag

upper sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 8
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 7
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattatacgcccttctacacagtagtaatatttatgtaaattct--tttgcactataagataaatatattcagcatttgaaaaacatttatcag--------
 ||||||||||||||||||| || || || ||| |||| ||||||||||| ||||| ||| |||||    |   |||     |   || |||  ||||    | |  ||||   |  ||  |   | | ||     |||||    | ||| |           
CAAATCAAGAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTGgtacatta----ctactctctgtggccatattatccatgttgcatgtaatttgtggttcaacttctgt-tctttgttgtttgatggtcgtttctggtatgcctaa

upper sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 8
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 5'ss of exon 8
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattatacgcccttctacacagtagtaatatttatgtaa-------attcttttgcactat-----aagataaatatatt--cagcatttgaaaaacatttatcag------------
 |||| || ||||||||||| || |||||||||||||||||  ||||||| ||||||||||| ||  |    |  || ||   |  |||| | | || |         ||||||     |||     || |   |||||||  || ||| | |||    | | |               
CAAATAAAAAACCCCAACTACAAGGGAAAATGGAAGGCACCTATGATTGACAACCCAGgttc-ttgcatattccacttcaacattttaatttgtttgcagtcttggtgttctttaatgttattttctaatactgatatattttcaacatcttaaatttgtgtgttttttgcctttttag

upper sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 8
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 8
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcat-tatacgc-ccttctacacagtagtaatatttatgtaaattcttttgcactataagataaatatattcagcatttgaaaaacatttatcag
||||| ||||| |||||||| || |||||||||||||||||| ||||||| ||||||||||| | |  | || ||| || |      |  ||| |||| |   ||  ||||  ||  || ||  | | | | |  |  ||   |  ||||  |||
AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatccatgcacctgcttcttctatgccatagttatttt--ttggtttggtct-caacattcagacacttataaactgttca-tattttacag

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|298193745|gb|HO040393.1|HO040393
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATA
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATA
EST: gi|13790097|gb|BG652688.1|BG652688
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAN                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|7147510|gb|AW509432.1|AW509432
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATNTCAAGGATGACCCCGACCTATATGTNTTTCCC-AACTTGAAGTACGTG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGT-TTTCCCCAACTTGAAGTACGTG
EST: gi|5606713|gb|AI900811.1|AI900811
EST:     TATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: TATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|193341174|gb|FK306414.1|FK306414
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|24136456|gb|BU926966.1|BU926966
EST:     GAACCCCAAGTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCC
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCC
EST: gi|208317285|gb|GE117494.1|GE117494
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|208091443|gb|GD886338.1|GD886338
EST:     GAGCCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTATGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|26045988|gb|CA783372.1|CA783372
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|208268672|gb|GE072089.1|GE072089
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCG
EST: gi|22524331|gb|BU083142.1|BU083142
EST:     AACCCCAACTATAAAGGAAAATGGAAAGCACCATTGATTGATAAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTATCCCCAACTT
genomic: AACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAA-CCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattatacgcccttctacacagtagtaatatttatgtaaattcttttgcactataagataaatatattcagcatttgaaaaacatttatcag

- - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - TGGAAG