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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgcctcttcaattacatgatttctgattgttattcttatcttattttttgttacttaaattatcatgtgtattttgatattggatttgcttagtatcttgtgtataaattgtgcttgcagGTCCCACGTGGTCCAGGTGGCTCACGTGAATATATGGGAAGAGGCCCTCCACCAGGCACAGGTCGTTGTTTCAACTGTGGAATGGATGGTCACTGGGCAA

Basic information

species Zea mays
transcript GRMZM2G099317_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099317_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g02880.1 (Oryza sativa), 3'ss of exon 4
gtaagttgcctcttcaattacatgatt--tctgattgttattcttatcttattttttgttacttaaat--tatcatgtgtattttgatattggatttgcttagtatcttgtgtataaattgtgcttgcagGTCCCACGTGGTCCAGGTGGCTCACGTGAATATATGGGAAGAGGCCCTCCACCAGGCACAGGTCGTTGTTTCAACTGTGGAATGGATGGTCACTGGGCAA
||| | ||  |||||  || | |   |   |  ||  | |||||  | || || |||  ||   |  |  |      |  || |  || ||   ||  || |   |||| |  | |||||| || ||||||| ||||||||||| ||||| ||||||||||||||||| ||||| ||||| || || |||||||| ||||| |||||||| || ||||||||||||||||
gtatgctgt-tcttcggttgcttctctaagcacatcctgattctattttttttctttaatatgaagctgctgctgaattgatctgtattttttgttgactgatgctcttttcaacaaattgagcatgcagGTTCCACGTGGTCCTGGTGGTTCACGTGAATATATGGGGAGAGGACCTCCTCCTGGAACAGGTCGGTGTTTTAACTGTGGGATTGATGGTCACTGGGCAA

upper sequence: GRMZM2G099317_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g17710.2 (Oryza sativa), 3'ss of exon 4
-----------gtaagttgcctcttcaattacatgat--ttctgattgttattcttatcttattttttgttact--taaatt-atcatgtgtattttgatattggatttgcttagtatcttgtgtataaattgtgcttgcagGTCCCACGTGGTCC---AGGTGGCTCACGTGAATATATGGGAAGAGGCCCTCCACCAGGCACAGGTCGTTGTTTCAACTGTGGAATGGATGGTCACTGGGCAA
            |  ||||| |    ||  ||||  |  | || |||  | |||||   | || |  || | ||  | |||| || || |||| |||  | |||| | || |  || |||| |  | ||||||||| ||||||| ||||||||| |    ||||| ||||||||||||||||| ||||| ||||| ||||| |||||||| ||||| |||||||| || |||||||||||||   
gtaagcagttctttggttgcattcctaagcacatcctgatactaatttattttcttccttcatgtcatgctgctgctgaattgattatctgtacttt--tgttggctctgat--gt-tcttttcaaaaaattgtgcatgcagGTTCCACGTGGTGCTGCTGGTGGTTCACGTGAATATATGGGGAGAGGACCTCCTCCAGGAACAGGTCGCTGTTTTAACTGTGGGATTGATGGTCACTGGG---

upper sequence: GRMZM2G099317_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g17710.1 (Oryza sativa), 3'ss of exon 4
gtaagttgcctcttcaattacatgat--ttctgattgttattcttatcttattttttgttact--taaatt-atcatgtgtattttgatattggatttgcttagtatcttgtgtataaattgtgcttgcagGTCCCACGTGGTCCAG---GTGGCTCACGTGAATATATGGGAAGAGGCCCTCCACCAGGCACAGGTCGTTGTTTCAACTGTGGAATGGATGGTCACTGGGCAA
    ||||| |    ||  ||||  |  | || |||  | |||||   | || |  || | ||  | |||| || || |||| |||  | |||| | || |  || |||| |  | ||||||||| ||||||| ||||||||| | |   |||| ||||||||||||||||| ||||| ||||| ||||| |||||||| ||||| |||||||| || |||||||||||||   
----gttgcattcctaagcacatcctgatactaatttattttcttccttcatgtcatgctgctgctgaattgattatctgtacttt--tgttggctctgat--gt-tcttttcaaaaaattgtgcatgcagGTTCCACGTGGTGCTGCTGGTGGTTCACGTGAATATATGGGGAGAGGACCTCCTCCAGGAACAGGTCGCTGTTTTAACTGTGGGATTGATGGTCACTGGG---

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|148954856|gb|EC900331.2|EC900331
EST:     ATGGCAGGGATGTCGATGGAAGTCGCATTGTTGTTGAGTTTGCTAAAGGG                         GTCCCACGTGGTCCAGGTGGCTCACGTGAATATATGGGAAGAGGCCCTCCA
genomic: ATGGCAGGGATGTCGATGGAAGTCGCATTGTTGTTGAGTTTGCTAAAGGGgtaagttgcc ... gtgcttgcagGTCCCACGTGGTCCAGGTGGCTCACGTGAATATATGGGAAGAGGCCCTCCA
EST: gi|14245050|gb|BG873632.1|BG873632
EST:     ATGGCAGGGATGTCGATGGAAGTCGCATTGTTGTTGAGTTTGCTAAAGGG                         GTCCCACGTGGTCCAGGTGGCTCACGTGAATATATGGGAAGAGGCCCTCCA
genomic: ATGGCAGGGATGTCGATGGAAGTCGCATTGTTGTTGAGTTTGCTAAAGGGgtaagttgcc ... gtgcttgcagGTCCCACGTGGTCCAGGTGGCTCACGTGAATATATGGGAAGAGGCCCTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtattttgatattggatttgcttagtatcttgtgtataaattgtgcttgcagGTCCCACGTGGTCCAGGTGGCTCACGTGAATATATGGGAAGAGGCCCTCCACCAGGCACAGGTCGTTGTTTCAACTGTGGAATGGATGGTCACTGGGCAA
      ttttgat  putative branch site (score: 4)
     attttgatatt  TA-rich tract