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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatattccaaactatggatttgcttttctgattgctggtttgatcaatttctcttgaagctctgcggtaactcaacttgctattgggttattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACCCATGGTGTCAG

Basic information

species Zea mays
transcript GRMZM2G065757_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065757_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 8
gtttgtatattccaaactatggatttgcttttctgattgctggtttgatcaatt-tctcttgaagctctgcggtaactcaacttgctattgggttattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACCCATGGTGTCAG
         ||   || |   | ||   |||||||    | | |||  |||||| | ||||  |    ||   |||  |||||| ||   || |||| ||||||||||| ||| | || ||||| ||||||||||||||||| ||||||||||| |  |||||||| ||
--------gtttgtaattt--gcttcaattttctggaaacagcttttgtcaattatatctttga----tgaattaaaacaactttctg--ggattatgttgcagACACAGCCATCAAAAATCTGCTCTCAGGTTGGTCTGTGTACTTTTGATGGGAAGCATGGTGTTAG

upper sequence: GRMZM2G065757_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT1G11910.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtatattccaaactatggatttgcttttctgattgctggtttgatcaatttctcttgaagctctgcggtaactcaacttgctattgggttattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACCCATGGTGTCAG
||| || |  |   ||   |||| | |||  |   ||   ||    | |||  | || |  ||  | |   |     | | |               |||||||| |||||   ||| ||||| || ||| |||||||||| ||||||||||| |||| |||||||||
gttagtgtgctt--aatattggactagctaataaaatctgtgacaag-tcatatgctgtgcaaattattttggcttaccattcatcccccttgcgccttgcagACCCAACCGAAGAAAATCTGCTCGCAGATTGGTCTGTGTACTTTTGATGGTACCCGTGGTGTCAG
















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|213184093|gb|FM191578.1|FM191578
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|67017226|gb|CO445975.1|CO445975
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|31354952|gb|CD439309.1|CD439309
EST:     CTGTTGTTTCTCAATATTGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|116816042|gb|EC858742.1|EC858742
EST:     CTGTTGTTTCTCAATATGGACAGCAGAT-CTA-ATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatttctcttgaagctctgcggtaactcaacttgctattgggttattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACCCATGGTGTCAG
                     cggtaac  putative branch site (score: 3)
                                            ttatttt  putative PPT
                                            ttatttt  TA-rich tract