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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacgacaggcatggtagttatttcatctcgtttgcattaaggcactagttactatactgcaaattgattctgtggcctttgctgactttgttcttgccagGTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCTATTTGGGAGGTCTGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATC

Basic information

species Zea mays
transcript GRMZM2G078458_T04
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078458_T04 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g03676.1 (Oryza sativa), 3'ss of exon 13
aacgacaggcatggtagttatttcatctcgttt---gcatta------aggcac-tagttactatactgcaaattgattctgtggcctttgctgactttgttcttgccagGTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCTATTTGGGAGGTCTGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATC---------
         |||  || ||||||   || ||||   ||||||      | |  | || ||| |  |  | ||||||||| |        |  ||| | ||||| ||  || |||||| || |||||| |||||         ||  | | |||  |||||||| ||||||||| | |||||| | || |||||| |||||||||||||||         
--------acatattatttattttccctagttttcagcattattctgtatgagcatatttatttcatggtaaattgattgtagaaatcct-ttgaatctgttcgtgt-agATTGGATCTAATGAAGATAGAGA---------TGATGAGCTCCGGAGTGCTATATGGGAGGTCAGTGGTGATAATGGAGCACTGAGTTTGCTTGTGGATCTTCTTAGAG
















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|74241323|gb|DT649237.1|DT649237
EST:     TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAG                         GTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
genomic: TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAGgttagcactt ... ttcttgccagGTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
EST: gi|110940705|gb|EE160862.1|EE160862
EST:     TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAG                         GTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
genomic: TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAGgttagcactt ... ttcttgccagGTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
EST: gi|211219812|gb|FL295368.1|FL295368
EST:     TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAG                         GTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
genomic: TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAGgttagcactt ... ttcttgccagGTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
EST: gi|166619822|gb|EG205168.1|EG205168
EST:     TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAG                         GTTGGATATAGTGAAGACAGAGAAAC
genomic: TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAGgttagcactt ... ttcttgccagGTTGGATATAGTGAAGACAGAGAAAC
EST: gi|71766034|gb|DR963971.1|DR963971
EST:     TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAG                         GTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
genomic: TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAGgttagcactt ... ttcttgccagGTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
EST: gi|148953146|gb|EE152627.2|EE152627
EST:     TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAG                         GTGGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
genomic: TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAGgttagcactt ... ttcttgccagGTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
EST: gi|71761805|gb|DR959742.1|DR959742
EST:     TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAG                         GTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
genomic: TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAGgttagcactt ... ttcttgccagGTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
EST: gi|86473471|gb|DY239841.1|DY239841
EST:     TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAG                         GTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT
genomic: TTGCCATGCAAGAACATGAGCTTGAACAGGTTGCTTCTTTACTTGGAGAGgttagcactt ... ttcttgccagGTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttactatactgcaaattgattctgtggcctttgctgactttgttcttgccagGTTGGATATAGTGAAGACAGAGAAACATCTTGTGCAGCGATCCAAAGTGCTATTTGGGAGGTCTGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATC
                                  tgctgac  putative branch site (score: 2)
                                        ctttgttctt  CT-rich tract
               aaattgatt  TA-rich tract