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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccgtctccccagtcctttttagcttcctttcccacggtgatctggttgtcgctatcggtcgcgcggtttcgatgcgatcgcggcctcgtgggtttgctctggctgatcagtgttcgtttggtttctgggcagGTGACCGTTGCCTACAACAAGGATCCCAGCCCCGTGAAGGTCAACCTCGGGGTCGGCGCCTACCGGACCGAG

Basic information

species Zea mays
transcript GRMZM2G094712_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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
















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|18385028|gb|BM418227.1|BM418227
EST:     CCTCCGTCTTCGCCGCACTCGAGCAGGCCCCGGAGGACCCCATCCTCGGA                         GTGACCGTTGCCTACAACAAGGATCCCAGCCCCATGAAGGTCAACCTCGGG
genomic: CCTCCGTCTTCGCCGCACTCGAGCAGGCCCCGGAGGACCCCATCCTCGGAgtaagtccgt ... ttctgggcagGTGACCGTTGCCTACAACAAGGATCCCAGCCCCGTGAAGGTCAACCTCGGG
EST: gi|211351968|gb|FL217074.1|FL217074
EST:     CCTCCGTCTTCGCCGCACTCGAGCAGGCCCCGGAGGACCCCATCCTCGGA                         GTGACCGTTGCCTACAACAAGGATCCCAGCCCCGTGAAGGTCAACCTCGGG
genomic: CCTCCGTCTTCGCCGCACTCGAGCAGGCCCCGGAGGACCCCATCCTCGGAgtaagtccgt ... ttctgggcagGTGACCGTTGCCTACAACAAGGATCCCAGCCCCGTGAAGGTCAACCTCGGG
EST: gi|16137337|gb|BI894202.1|BI894202
EST:     CCTCCGTCTTCGCCGCACTCGAGCAGGCCCCGGAGGACCCCATCCTCGGA                         GTGACCGTTGCCTACAACAAGGATCCCAGCCCCATGAAGGTCAACCTCGGG
genomic: CCTCCGTCTTCGCCGCACTCGAGCAGGCCCCGGAGGACCCCATCCTCGGAgtaagtccgt ... ttctgggcagGTGACCGTTGCCTACAACAAGGATCCCAGCCCCGTGAAGGTCAACCTCGGG
EST: gi|61119383|gb|DN560344.1|DN560344
EST:     CAGGCCCCGGAGGACCCCATCCTCGGA                         GTGACCGTTGCCTACAACAAGGATCCCAGCCCCGTGAAGGTCAACCTCGGG
genomic: CAGGCCCCGGAGGACCCCATCCTCGGAgtaagtccgt ... ttctgggcagGTGACCGTTGCCTACAACAAGGATCCCAGCCCCGTGAAGGTCAACCTCGGG
EST: gi|18385008|gb|BM418207.1|BM418207
EST:     CCTCCGTCTTCGCCGCACTCGAGCAGGCCCCGGAGGACCCCATCCTCGGA                         GTGACCGTTGCCTACAACAAGGATCCCAGCCCCATGAAGGTCAACCTCGGG
genomic: CCTCCGTCTTCGCCGCACTCGAGCAGGCCCCGGAGGACCCCATCCTCGGAgtaagtccgt ... ttctgggcagGTGACCGTTGCCTACAACAAGGATCCCAGCCCCGTGAAGGTCAACCTCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcggcctcgtgggtttgctctggctgatcagtgttcgtttggtttctgggcagGTGACCGTTGCCTACAACAAGGATCCCAGCCCCGTGAAGGTCAACCTCGGGGTCGGCGCCTACCGGACCGAG
                       ggctgat  putative branch site (score: 4)
                                            tttct  putative PPT