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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCGCCGACGCCGACTCCTCCCTCCAAGCTTTCCCCACCATGGCGTCGTCGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccccctctcgtctcccaatctcactcccgctccccatcgctgtcttcaccggtttcggccgtgatcgcgcggttttttgggttcgctcgacctgatcggtgctcccgttggtgttgtggtag

Basic information

species Oryza sativa
transcript LOC_Os01g55540.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55540.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G094712_T06 (Zea mays), 5'ss of exon 1
CGCCGCCGACGCCGACTCCTCCCTCCAAGCTTTCCCCACCATGGCGTCG------TCGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccccctctcg---tctcccaatctcactcccgctccccatc--gctgtcttcaccggtttcg--gccgtgat-cg--cgcggttttttgggttcgctcgacctgatcggtgctcccgttggtgttgtggtag
      |  ||||  |||| ||||| || | ||||||||||||||||||      || ||||||||||| |  |||| |||||| |||||||||||||||||||| |||||  |  |  | |      |   |   ||  | ||       |||  | ||||   | ||||  ||  |    ||| ||  |||||  |  |||||| ||||   |||||| ||| ||   ||||| |   || ||
------CTCCGCCACCTCCACCCTCGAATCGTTCCCCACCATGGCGTCGCAGGGATCCTCCGTCTTCGCCGCACTCGAGCAGGCCCCGGAGGACCCCATCCTCGGAgtaagtccgtctccccagtcctttttagcttcctttcccacggtgatctggttgtcgctatcggtcgcgcggtttcgatgcgatcgcggcctcgtgggtttgctctggctgatcagtgttcgt-ttggtttctgggcag

upper sequence: LOC_Os01g55540.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G094712_T04 (Zea mays), 5'ss of exon 1
CGCCGCCGACGCCGACTCCTCCCTCCAAGCTTTCCCCACCATGGCGTCG------TCGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccccctctcg---tctcccaatctcactcccgctccccatc--gctgtcttcaccggtttcg--gccgtgat-cg--cgcggttttttgggttcgctcgacctgatcggtgctcccgttggtgttgtggtag
                                        |||||||||      || ||||||||||| |  |||| |||||| |||||||||||||||||||| |||||  |  |  | |      |   |   ||  | ||       |||  | ||||   | ||||  ||  |    ||| ||  |||||  |  |||||| ||||   |||||| ||| ||   ||||| |   || ||
----------------------------------------ATGGCGTCGCAGGGATCCTCCGTCTTCGCCGCACTCGAGCAGGCCCCGGAGGACCCCATCCTCGGAgtaagtccgtctccccagtcctttttagcttcctttcccacggtgatctggttgtcgctatcggtcgcgcggtttcgatgcgatcgcggcctcgtgggtttgctctggctgatcagtgttcgt-ttggtttctgggcag
















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|32948428|gb|BP185000.1|BP185000
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|88695330|gb|CI737833.1|CI737833
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|33685641|gb|CF313880.1|CF313880
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|44667509|gb|CR280943.1|CR280943
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|58591056|gb|CF989364.1|CF989364
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGTCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|29639571|gb|CB644580.1|CB644580
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|32948311|gb|BP184883.1|BP184883
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|88723781|gb|CI747291.1|CI747291
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|58656014|gb|CK044694.1|CK044694
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|29679665|gb|CB675940.1|CB675940
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|29660055|gb|CB656330.1|CB656330
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|32948296|gb|BP184868.1|BP184868
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|218478855|gb|FG949686.1|FG949686
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|29658837|gb|CB655112.1|CB655112
EST:     CGTCCGTCTTCGCTGGCCTCGCGCACGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|58694708|gb|CK083395.1|CK083395
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|33793380|gb|CF322571.1|CF322571
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|33795088|gb|CF323417.1|CF323417
EST:     GGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: GGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
EST: gi|58669037|gb|CK057723.1|CK057723
EST:     CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGG                         GTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC
genomic: CGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccc ... gttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCCGCCGACGCCGACTCCTCCCTCCAAGCTTTCCCCACCATGGCGTCGTCGTCCGTCTTCGCTGGCCTCGCGCAGGCGCCGGAGGACCCCATCCTCGGGgtaagatccccctctcgtctcccaatctcactcccgctccccatcgctgtcttcaccggtttcggccgtgatcgcgcggttttttgggttcgctcgacctgatcggtgctcccgttggtgttgtggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA