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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaatgtaataattcatgaagatattgttccttatgttcatggtgtttgttttgttaggattttatgctttcagtttctgtttccttaacaaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG

Basic information

species Zea mays
transcript GRMZM2G131324_T01
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 3
acaatgtaataattcatga-agatattgttcctta-----tgttcatggtg-tttgttttgttaggattttatgctttcagtttctgtttccttaacaaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG
   ||  ||   ||  |   | ||  |||  || |       || |||||  | |  |||  |||||||||||||| ||||||     |||||||| ||||||  ||||||||||||||||  |||||||||||||| ||||| || || |||   ||  | |||||||| |||||||||||||||||||| |
---ataaaacccttggtattatatcatgtctctgagaggacatttatggtaatattatttaataggattttatgctgtcagttg----ttccttaagaaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGAGGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAG

upper sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 3
acaatgtaataat-tcatgaagat----attgttccttatgttcatggtgtttgttttgttaggattttatgctttcagtttctgtttccttaacaaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG
 |   ||| |||| |||||   ||    |  |    |||||   ||  | ||| |||  | ||||||||||||| ||||||     |||||||| ||||||  ||||||||||||||||  |||||||||||||| ||||| || || ||    ||  | |||||||| |||||||||||||||||||| |
ccttggtattaatatcatgtcaatctaaagaggatgttatgggtatattttttatttaat-aggattttatgctgtcagttg----ttccttaagaaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAG
















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|67031739|gb|CO460488.1|CO460488
EST:     ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATTTACTGCATGGA                         GCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
genomic: ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgtt ... aaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
EST: gi|32931459|gb|CF036271.1|CF036271
EST:     ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATTTACTGCATGGA                         GCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
genomic: ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgtt ... aaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
EST: gi|26456742|gb|CA828325.1|CA828325
EST:     ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGA                         GCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
genomic: ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgtt ... aaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
EST: gi|32934477|gb|CF039289.1|CF039289
EST:     ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATTTACTGCATGGA                         GCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
genomic: ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgtt ... aaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttttgttaggattttatgctttcagtttctgtttccttaacaaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG
                                    ttccttaac  putative branch site 
                                        ttaacaaaa  TA-rich tract