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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatccccctctcgtctcccaatctcactcccgctccccatcgctgtcttcaccggtttcggccgtgatcgcgcggttttttgggttcgctcgacctgatcggtgctcccgttggtgttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG

Basic information

species Oryza sativa
transcript LOC_Os01g55540.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G094712_T04 (Zea mays), 3'ss of exon 1
gtaagatccccctctcg---tctcccaatctcactcccgctccccatc--gctgtcttcaccggtttcg--gccgtgat-cg--cgcggttttttgggttcgctcgacctgatcggtgctcccgttggtgttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG
|||||  |  |  | |      |   |   ||  | ||       |||  | ||||   | ||||  ||  |    ||| ||  |||||  |  |||||| ||||   |||||| ||| ||   ||||| |   || ||||||| || || |||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||
gtaagtccgtctccccagtcctttttagcttcctttcccacggtgatctggttgtcgctatcggtcgcgcggtttcgatgcgatcgcggcctcgtgggtttgctctggctgatcagtgttcgt-ttggtttctgggcagGTGACCGTTGCCTACAACAAGGATCCCAGCCCCGTGAAGGTCAACCTCGGGGTCGGCGCCTACCGGACCGAG
















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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcggttttttgggttcgctcgacctgatcggtgctcccgttggtgttgtggtagGTGACGGTCGCGTACAACAAGGATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG
                      acctgat  putative branch site (score: 4)
     tttttt  TA-rich tract