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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgcaccatgcctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccatgtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT

Basic information

species Zea mays
transcript GRMZM2G098078_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 5
---tgctgcaccatgcctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccatgtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT
         |  ||   | | ||| |   ||   || |   ||  | ||| |  |    || |  |   | || ||   |  ||  | | || ||||  |||||||||||| ||||||||||| |  ||||| ||||||||||||||  |||||||||||||||  |||||||| ||||||||||| ||||| |||||||| |
tagaaagtaagaattggtactctttaatatcagggaaattcaacatgatagagggagatatatacc-atacttctttttacatacttatgttccttt--gcagCAATTTGAATGGTTAGTTGGAACACAATATAAGCCAATGGAGCTAACAAAGTCAGATTGGGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCT

upper sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 5
tgctgcaccatg-cctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccatgtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT
  |    | | |   ||     ||  ||  ||| |  | ||| ||| || |  || || |  |   |  |  |    ||   |    | || | | | ||||||| ||  ||| | |||||    |||||||| |||||||| ||| |||| || || |||||| ||||||  || || ||||| ||||||||||||||||
gaccttgcaaggatttgtgaggcatttttattgttttaaaaaataaaaaga-attcaagtagtgaaacctaatatatattcctcacatgttttctattcagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAATCTGACTGGGCTGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT

upper sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 5
tgctgcaccatgcctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccat--gtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT
  |      |||  |     |    ||| ||  |  | ||   |  | |  |  ||      |  || |||| | ||   || |   |  ||| | || ||||||| ||  ||| | |||||    |||||||| ||||||||| || |||| ||||| |||| | ||||||  || || ||||| ||||||||||||||||
-cccttgtaatgatttgatctgggcttctttattttaaaataaaggatatggaatagggaaaccaaaattgtcctcacaagttttcatgcttcctgtt-cagCAATATGCATGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT

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|211086448|gb|FL450103.1|FL450103
EST:     TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTG                         CAATTTGAGTGGTTAGTTGGGATGCAA
genomic: TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggactt ... ctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAA
EST: gi|76289771|gb|DV029339.1|DV029339
EST:     TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTG                         CAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAG
genomic: TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggactt ... ctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAG
EST: gi|211352110|gb|FL449964.1|FL449964
EST:     TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTG                         CAATTTGAGTGGTTAGTCGGGAT
genomic: TTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggactt ... ctttttgcagCAATTTGAGTGGTTAGTTGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatgtttaatttctctgaatttgttcccatgtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT
      gtttaat  putative branch site (score: 4)
                                    tgtgtttttcttttt  putative PPT
                                        tttttcttttt  TA-rich tract