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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtcctttcgtttagctcctgcgctttgtacagtttggaacagctaactatgggctcacatttctttttcactactgtgatgattag

Basic information

species Oryza sativa
transcript LOC_Os02g13990.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G24350.2 (Glycine max), 5'ss of exon 7
GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtcctttcgtttagctcctgcgctttgtacagtttggaacagcta------actatgggctcacatttctttttcactactgtgatgattag--
||||||||||||||||||||||| ||||| |||||||| || |||||||||||      |  | |   |||| |  |  | ||  |  | |||       ||       |||   |  | ||||    ||   | |||||| |  | ||   
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgcttttctaaattagataat-tgtttaatggattttaatgtttctgtgtcatactcatgcttaacatgatattgaaattactgtaaacaatatga

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G18440.1 (Glycine max), 5'ss of exon 7
GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtcctttcgtttagctcctgcgctttgtacagtttggaacagctaactatgg-gctcacatttctttttcactactgtgatga--ttag-----
||||||||||||||||||||||| ||||| |||||||| ||||||||||||||  |   |  | |   |||| |  |  ||||  |  | |||        |   | |    ||||   ||   ||  | || ||  || |  |||      
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgcctgcttttctaaattagataat-tgcttattggattttaatgtttgtttgtgtaatactcatgcttaacttagaatattgaaattacattaaataat

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv01s0150g00590.t01 (Vitis vinifera), 5'ss of exon 6
GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtcctttcgtttagct---cctgcgctttgtacagtttggaacagctaactatgggctc---acatttctttttcactactgtgatgattag----
|| || ||||||||||| ||||| ||||| |||||||||||||||||||||||    |   |||| |||||  |   | ||   ||  |   ||||   |  | | | | |    |    |||     ||||||      |  || || |    
GCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAGgtgctgt---cttttgtttaattagacttggatttcattttgtttttcaatgtttattctttatttttaacaccatgttttcatatgaattgtgcttgggtag

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S134_26V6.2 (Physcomitrella patens), 5'ss of exon 5
-------------------------------------------------GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgta-gcatgtcctttc---------------gtttagctcctgcgctttgtacagtttggaa--cagctaactatgggctcacatttctttttcactactgtgatgattag----------------------------
                                                  |||||||||  |||||||||||||| || || ||||| ||||| ||||||||| |  ||   | ||                 |||| | ||    |||| |   | | |    || |  |          |    || || |   |  | |  |  || |                            
GTTATTTCTCGCAAGAATCCTTACCTGGTAGTCTTTCCTTGTGATTCAGACTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgctttatctacctgcctaatgaaacttagtttctctcttttgcattatcttgtgttcatcgtatctcaaaaagaagcgtccttgtattttatattgtatttcgtgcattgaaagaagttgatttcgtgcag

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S49_103V6.1 (Physcomitrella patens), 5'ss of exon 7
GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgta----------gcatgtcct------ttcgtttagctcctgcgctttgtacagtttggaacagctaactatgggctcacatttctttttcactactgtgatgattag---------------------------------------------
 | || ||||  ||||||||||| ||||| ||||| || |||||||||||||||          | || |  |      ||   ||  ||  | |  |||      |||        | | || |  | ||   |||  ||   |    ||||   ||                                               
ACCGCTATTGCAAATTCTCAGACGCTTGAAGAGGTCGCCAGGCTTGAAAAGgtactactgctcggtatattttaggaaattgagtttccttttactttttacttgattttagttcaatcattaagttcacaacattcagttatgccgtggtgaatttttatttggcacattgtgcatgcattgagatcttatttttcttttgcag

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S152_48V6.2 (Physcomitrella patens), 5'ss of exon 8
GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagca-tgtcctttcgtttagctcctgcgctttgta-----cagtt-------tggaacagctaactatgggctcacatttctttttcactactgtgatgattag-------------------------------------------
 ||||||| |  ||||| ||||||||||| || ||||| |||||||||||||||||| |||        |    |  ||     || |      | ||       || ||||  |   | | |  |   | || |   |||     |||    |||                                            
ACTGCCATCGCAAATTCACAGACACTTGAAGAAGTTGCCAGGCTTGAAAAGgtagcactgtttgggaaatccatttttggaaactgaaatcactaattccttcagtgcaacatttttatgttgtatgcaacttttcgctcaacttcgtgggttttacaagtttgttgtgcatacattgaaatcgaaattatcttctgcag

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S134_26V6.1 (Physcomitrella patens), 5'ss of exon 6
GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgta-gcatgtcctttc---------------gtttagctcctgcgctttgtacagtttggaa--cagctaactatgggctcacatttctttttcactactgtgatgattag----------------------------
 |||||||||  |||||||||||||| || || ||||| ||||| ||||||||| |  ||   | ||                 |||| | ||    |||| |   | | |    || |  |          |    || || |   |  | |  |  || |                            
ACTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgctttatctacctgcctaatgaaacttagtttctctcttttgcattatcttgtgttcatcgtatctcaaaaagaagcgtccttgtattttatattgtatttcgtgcattgaaagaagttgatttcgtgcag

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|29681479|gb|CB677754.1|CB677754
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|88201604|gb|CI201959.1|CI201959
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86500192|gb|CI142825.1|CI142825
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86545114|gb|CI185320.1|CI185320
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|88227188|gb|CI228301.1|CI228301
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86500747|gb|CI143380.1|CI143380
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86421117|gb|CI057106.1|CI057106
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|88223253|gb|CI223102.1|CI223102
EST:     AAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: AAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86536011|gb|CI176217.1|CI176217
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|29645677|gb|CB650684.1|CB650684
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86503360|gb|CI145993.1|CI145993
EST:     TGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: TGCCATTGTGAATTCTCAGACACTTGAGGAGGTTG-CAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|88225868|gb|CI225784.1|CI225784
EST:     TGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: TGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|5005007|gb|AU068324.1|AU068324
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|88223197|gb|CI223046.1|CI223046
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|88830705|gb|CI078149.1|CI078149
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         ACACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|88252358|gb|CI350786.1|CI350786
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86505850|gb|CI148483.1|CI148483
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|88460872|gb|CI553008.1|CI553008
EST:     GAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: GAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|116875219|gb|EC365727.1|EC365727
EST:     CTGCCATTGTGAATCCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86541745|gb|CI181951.1|CI181951
EST:     CCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86496623|gb|CI139256.1|CI139256
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86540436|gb|CI180642.1|CI180642
EST:     GCAAGGCTTGAAAAG                         GCACTGAGCACTGGTCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: GCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
EST: gi|86500143|gb|CI142776.1|CI142776
EST:     CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG                         GCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT
genomic: CTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtc ... tgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtcctttcgtttagctcctgcgctttgtacagtttggaacagctaactatgggctcacatttctttttcactactgtgatgattag

- - - - - - - - - - - - -  GAGGAG