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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatttgaatgctttttgtgccaaaagtgttcacaaacttaaccatctagcccaatttatcatctttaaggttcgttattctttgcttaactgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCATTTGGTTCTTTGCAT

Basic information

species Zea mays
transcript GRMZM2G070113_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070113_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g36120.1 (Oryza sativa), 3'ss of exon 6
-caaatttgaatgctttttgtgccaaaagtgttcacaaacttaaccatctagcccaatttatcatctttaaggttcgttattctttgcttaactgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCATTTGGTTCTTTGCAT
    |  || || | | |    |    | |    |   |   ||    | | |   | |  |        |  ||  ||    |||| ||   |||||||||||||||||| ||||| |||| ||| || | |||||||||| |||| ||||||||| ||||||||
tagtacatgtattcatctcccactggga-taaataagtatggaatttcccaccgataatgcttgcaaagtatatttattgcattttgtttgtttgatgcagGTTTTCAAGCCCTTATCCAGTATCAGTCACTCCAAGAAGCTATGGATGCATTTGGTGCTTTGCAT
















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|67016395|gb|CO445144.1|CO445144
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|31628085|gb|CD526434.1|CD526434
EST:     CAAAGCTTATGGATTTGTTGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|30031872|gb|CB833723.1|CB833723
EST:     TTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: TTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|61118021|gb|DN558982.1|DN558982
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|31360867|gb|CD445224.1|CD445224
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|71436418|gb|DR817468.1|DR817468
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|76011812|gb|DT938982.1|DT938982
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctagcccaatttatcatctttaaggttcgttattctttgcttaactgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCATTTGGTTCTTTGCAT
                                            aactgat  putative branch site (score: 3)
         aatttatcatctttaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaatttgaatgctttttgtgccaaaagtgttcacaaacttaaccatctagcccaatttatcatctttaaggttcgttattctttgcttaactgatgcagGTTTTCAAGCTCTTATTCAGTTTCACTCGCGCCAAGAAGCTGTGGAAGCATTTGGTTCTTTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG