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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata...

Basic information

species Oryza sativa
transcript LOC_Os11g29190.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G156673_T02 (Zea mays), 5'ss of exon 1
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgta-accccccctttcgcgcttcgctcgcccaatctctttcgaacca-gtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata
|| ||||||| || |||||| |||||||  || |||||||||||||||| |||||||| ||||||||||| |||||| |||||||||| |||||||||||||| |  |    | |||         ||   || ||  |    || |  |     ||        | || | || | || |  || |   | | ||    | 
AGGTCATGGCTGTCCGCATCATCAAGCATACCCTGGAGATCATCCACCTGCTCACCGATGCCAACCCCATCCAGGTCGTCGTCGACGCGATCATCAACAGgtacagtcttaatctcggctaataaccgttaaacctactcgttactatatgttgattccattcagtatgctggatccccccctga-accgtgtgtgtattt-

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G078985_T01 (Zea mays), 5'ss of exon 2
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata---
|| |||||||||| |||||| | |||||| || |||||||||||||||| ||||| |||||||| ||||| |||||  |||| |||||||| |||||||||||   ||    |   |  | | | | ||| |||||| |     |||   |||   | |   | ||||||   |   |  |    | || |  ||        
AGGTCATGGCCGTCCGCATCATGAAGCACACCCTGGAGATCATCCACCTGCTCACTGACGCCAATCCCATCCAGGTGGTCGTGGACGCCATTATCAACAGgtactaccttgctctcctgtcctcactcccgatctctgtattgtcaggctaataacagctaaacttgtta---ctttatgctgatactttttggaatgcggta

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G26840.2 (Glycine max), 5'ss of exon 3
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata--------
|| ||||||| ||  | ||  ||||||| |||||||||||||||||| | ||||| |||   ||||| ||||||||||| || || ||| ||||||| |||||         |||| |  | |    |    | | ||| |      |  | ||     ||| |||  | | | |  |   |    |     ||  |  |        
AGCTCATGGCTGTCAGGATTATCAAGCATGCCATGGAGATCATCCACTTGCTCACTGACCTGAACCCAATTCAGGTCATTGTTGATGCCGTCATCAATAGgta-------tgttcgggtgttgagaacttc-ttttttttgtgttgatggatttgctttgggttttaattgcagatgagttgtttgtgctggtgtcatcaattgtaga

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT3G11940.2 (Arabidopsis thaliana), 5'ss of exon 3
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata
|  | ||||| ||  | ||||||||||||||||||||||| ||||||||| |  | |||   ||||| |||||||||||| | ||||||||  ||||||||||  |   ||||  |   |  |||     | | || || |||| || || ||||||       || |||           |    || | |        
AATTGATGGCTGTCAGGATCGTCAAGCACGCCATGGAGATTATCCACCTCTTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgta--ctaaccttgtgaagtatgctgaaatagtatcattggaacaaggaacattttatt----cttattaatgttttgtttgttgcttgagccag-----

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 3
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgta-accccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata-
|| | ||||| ||  | ||||||||||| ||||||||||| ||||||||| |  | |||   ||||| ||||| || ||| | || |||||  | |||||||| |       |      ||     |    ||  |||| ||  |  || |   |  || |    |  |||  |             ||||| ||| | || 
AGTTGATGGCTGTCAGGATCGTCAAGCATGCCATGGAGATTATCCACCTCTTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAGgtatattaagattgctatactgaaacctgtaaaattcttgcgtgcttgttactatgaactgaatctaattaagaaggtttgt---tctttatgtga-attag

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S101_208V6.1 (Physcomitrella patens), 5'ss of exon 2
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccct----ttc------------------gcgctt---cgctcgccca---atctctttcgaa-ccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata-------------------
|| | ||||| || |||||||| |||||||| |||||||| || ||||| || ||||||   ||||| || |||||||||||||||||||||||||||||||     | |      |||                   || ||    ||| |  |     | | ||  ||| |  | |||  |||   || |||  || | | |   |  | |  || |  | |||                      
AGTTGATGGCTGTACGCATCGTGAAGCACGCGATGGAGATTATTCACCTACTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctctcgaagttccatgaggtggcacgggagacgtttgaatgcttgggcgtgtgtgtgttgtgaagctgggaaaggtttttaggcattatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcag

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S114_143V6.1 (Physcomitrella patens), 5'ss of exon 2
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccg---ggatttgttagaacaccaca-cgagaattta----tctg-agaata---------------------------------------------
|| | ||||| ||||||||||| |||||||| ||||||||||||||||| || || |||   |||||||| ||||||||||| || |||||||||||||||||      | |    | |||   | ||   || |     | |   |       |   ||   ||    |     |     || |  |||||||    | ||  | ||                                              
AGTTGATGGCGGTGCGCATCGTGAAGCACGCGATGGAGATCATCCACCTGCTGACGGACCAGAACCCCATCCAGGTCATCGTGGATGCCATCATCAACAGgtaggttatc-tcgaacacttgtttagctgcatattggggggagaggcgggggatgggcgcatgggcgggaggagaggttgcaacaggaatttagggttatgcgggatgatgtggggctcgggagctgagaggtcgcggtgggaatgggtacag

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S400_33V6.1 (Physcomitrella patens), 5'ss of exon 2
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgt---aaccccccctttc-----gcgcttcgctcgcccaat---------ctctttcgaacc-agtaaaatt---ttaccgggatttgttagaacaccacacg-agaatttatctgagaata
|| | ||||| || ||||| || |||||||| ||||||||||| ||||| || || ||    |||||||| ||||||||||| || || |||||||||||||   || |    |||||     | | ||     |   |||         | || | ||  | |||  ||||   ||   |  |||| |     ||  |  |  |   ||||||||      
AGTTGATGGCTGTCCGCATTGTGAAGCACGCTATGGAGATCATTCACCTTCTGACTGATCAGAACCCCATCCAGGTCATCGTTGATGCTATCATCAACAGgtttgaatcttatctttctattggtgtttgatgtggaaaatgaaatgcgacactcttgaggcgagtctaattcaattgtagcaatttttagtggcatgaggcatatcttttatctgctgcag

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S10_385V6.1 (Physcomitrella patens), 5'ss of exon 2
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgt---aaccccccctttcgcgct-tcgctcgccca------atctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata---
|| | ||||| || ||||| || ||||||||||||||||| ||||| ||||| || |||   ||||||||||||||||||||||| || || ||||||||||    || |   |    | | | |||  |  ||       |    | |    |   | |||| ||  |    | | |  || |     ||     |||  |  | | |    
AGTTGATGGCTGTCCGCATTGTGAAGCACGCCATGGAGATTATCCATCTCCTGACTGACCAGAACCCCATTCAGGTCATCGTCGATGCTATTATCAACAGgttcggacgcaatcccgtgtgatatcgaacatcctgaggacacaattctttttctgattaaatattgtcaatttgtctctgagcg----acagtgttttcccatacattgcag

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata
|| | ||||| | |||||| || |||||||| ||||||||||| ||| | ||||| || || || || || ||  ||||||| ||||||||||||||||||||   |      || |  |       |   ||   |||     |  |     ||  | |                                        
AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgctt-gcag----------------------------------------

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 3
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata
|| | ||||| |  ||||| || ||||| || ||||||||||| ||| | ||||| ||||||||||| || ||  | || ||||| || ||||||||||||||          | | | |||    |  ||   |     ||     |   |||||  |    | | || | |                           
AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgta----------tagaggttcaagtgagcaggattccaggacagttttggattttctctctttctctttgcag--------------------------

upper sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ37091 (Selaginella moellendorffii), 5'ss of exon 3
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata
|| | ||||| |  ||||| || ||||| || ||||||||||| ||| | ||||| ||||||||||| || ||  | || ||||| || ||||||||||||||          | | | |||    |  ||   |     ||     |   |||||  |    | | || | |                           
AGTTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgta----------tagaggttcaagtgagcaggattccaggacagttttggattttctctctttctctttgcag--------------------------

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|58684408|gb|CK073095.1|CK073095
EST:     CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAG                         TGGCCCTCGTGAGGATGCGACC
genomic: CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaacccccc ... ttgtttgcagTGGCCCTCGTGAGGATGCGACC
EST: gi|2190306|gb|D15414.1|D15414
EST:     CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAG                         TGGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCGGGTGCTGTGAGGAG
genomic: CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaacccccc ... ttgtttgcagTGGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCGGGTGCTGTGAGGAG
EST: gi|218497395|gb|FG967337.1|FG967337
EST:     CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAG                         TGGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCGGGTGCTGTGAGGAG
genomic: CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaacccccc ... ttgtttgcagTGGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCGGGTGCTGTGAGGAG
EST: gi|58678824|gb|CK067511.1|CK067511
EST:     CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAG                         TGGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCGGGTGCTGTGAGGAG
genomic: CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaacccccc ... ttgtttgcagTGGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCGGGTGCTGTGAGGAG
EST: gi|5005367|gb|AU070529.1|AU070529
EST:     CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAG                         TGGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCNGGTGCTGTGAGGAG
genomic: CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaacccccc ... ttgtttgcagTGGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCGGGTGCTGTGAGGAG
EST: gi|286606|gb|D15413.1|D15413
EST:     CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAG                         TNGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCGGGTGCTGTGAGGAG
genomic: CTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaacccccc ... ttgtttgcagTGGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCGGGTGCTGTGAGGAG