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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGATGCCGATGAGGCCTGTGCGGCCAGGGCCGCCGATGCAGTACCGGGGGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctcctccgtgcccccctcccaatcgatgcgctggaacagcagtagattgcgtactaccttgcgattcgacggcattgtgttccagttcgattctgctaggttaaccatgttgattgatttgtttacttactgttcactatcgggttcttttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g02960.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02960.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G064988_T02 (Zea mays), 5'ss of exon 2
CGAGATGCCGATGAGGCCTGTGCGGCCAGGGCCGCCGATGCAGTACCGGGGGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc---ctccgtgcccccctcccaatcgatgcgctggaacagcagtagattgcgtactaccttgcgattcgacggcattgtgttccagttcgattctgctaggttaaccatgttgattgatttgtttacttactgttcactatcgggttcttttgcag
||| |||||||||||||||| |||||| || |||||||||||| |||| || || || || ||||| |||   |||  ||||||  |||| ||||||||||| ||  ||    | || | |||||||  |   ||  |    |   |  | || || || | |    |  ||||| |     | ||||| |  | | || |    |                                                           
CGATATGCCGATGAGGCCTGCGCGGCCGGGCCCGCCGATGCAGCACCGTGGTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttcttacaccccctcccccccttgctcccggcgtcaggcttctactgtggaatgtgaa---tcccgcgatgct----ccttgtggtggattgcgctctcaca----------------------------------------------------------

upper sequence: LOC_Os02g02960.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G060669_T04 (Zea mays), 5'ss of exon 2
CGAGATGCCGATGAGGCCTGTGCGGCCAGGGCCGCCGATGCAGTACCGGGGGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc---ctccgtgcccccctcccaatcgatgcgctggaacagcagtagattgcgtactaccttgcgattcgacggcattgtgttccagttcgattctgctaggttaaccatgttgattgatttgtttacttactgttcactatcgggttcttttgcag
||| |||||||||||||| | |||||| || |||||||||||| ||||||| ||||| || ||||| |||   |||  ||||||  |||| ||||||||||| ||  ||    |||| |||  ||| |    ||   | |   |     |     | |  || ||| ||   ||   | |  | |||||    | |  | ||   |                                                           
CGATATGCCGATGAGGCCGGCGCGGCCGGGCCCGCCGATGCAGCACCGGGGCCCTCCGCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttcttacactccttgcgtcccccttgctcatggtgtcagt----cttctaagtaagttctaactcatgagatgcc--ccttgtggcggattgtgctttcac-----------------------------------------------------------
















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|10930921|gb|AU161195.1|AU161195
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|58587706|gb|CF986014.1|CF986014
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|58603994|gb|CK014522.1|CK014522
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAACAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAA-AG
EST: gi|29659833|gb|CB656108.1|CB656108
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|88760807|gb|CI770363.1|CI770363
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|33660656|gb|CF291623.1|CF291623
EST:     GCCTCCTCCCATGGCTCGCGCGCGCTGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GCCTCCTCCCATGGCTCGCGCGCGC-GTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|88399521|gb|CI606142.1|CI606142
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|58664968|gb|CK053654.1|CK053654
EST:     CGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: CGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|88329643|gb|CI650106.1|CI650106
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|33659745|gb|CF282358.1|CF282358
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|88725672|gb|CI748931.1|CI748931
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|23514260|gb|BU673547.1|BU673547
EST:     GCCTTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GCC-TCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|88694523|gb|CI738561.1|CI738561
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|58590816|gb|CF989124.1|CF989124
EST:     TCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTGTCGTGCTCCGGGTTTTCACAAAG
genomic: TCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|27576068|gb|CA998762.1|CA998762
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|88352110|gb|CI613761.1|CI613761
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGGAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|33806035|gb|CF328897.1|CF328897
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|33658759|gb|CF281372.1|CF281372
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|88348144|gb|CI637605.1|CI637605
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|38468952|gb|CF953083.1|CF953083
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGATAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|33657430|gb|CF280044.1|CF280044
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|33653966|gb|CF276580.1|CF276580
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCNTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTC-TCCTGCTCCGGGTTTTCACAAAG
EST: gi|5667412|gb|AU077654.1|AU077654
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
EST: gi|4714342|gb|AU058309.1|AU058309
EST:     GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAG                         ACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG
genomic: GGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctc ... tcttttgcagACGTGCCCTCTCCTGCTCCGGGTTTTCACAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGATGCCGATGAGGCCTGTGCGGCCAGGGCCGCCGATGCAGTACCGGGGGCCTCCTCCCATGGCTCGCGCGCGCGTCGAACCCGTCGATCGCGAGAAGgtgaggcctcctccgtgcccccctcccaatcgatgcgctggaacagcagtagattgcgtactaccttgcgattcgacggcattgtgttccagttcgattctgctaggttaaccatgttgattgatttgtttacttactgttcactatcgggttcttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC