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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacttaatatagttccttggatgcatgtataatttatgactattttcaacatttggggcatagaggaataccttacaagttttctatatctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCTTCTGGGCATCT

Basic information

species Zea mays
transcript GRMZM5G846198_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846198_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 9
aaacttaata---tagttccttggatgcatgta---taattta--tgactattttcaacatttggggcatagaggaataccttacaagttttctatatctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCTTCTGGGCATCT
 ||  ||| |   |||||||    | || ||||   ||  |||  ||  ||| |||  ||||  | |  ||||   || | |||      || |  || ||||||||||||| ||| | | ||||||||||||| || || || || |||||||||||||||||||||||
-aaagtaacagattagttccactcaagcttgtaccttacattaagtggttatgttcttcattgtgtgt-tagaaatatccttta------ttgtgcatttttattcagGACCTTAAAGCTACAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCT
















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|32930138|gb|CF034950.1|CF034950
EST:     GTCTTATCACTGGTGATGCTTCATCAAAAAGTAAAGCTGATAAAACCACT                         GACCGTAAGGATGCAAGACAAGGGGAGACCATAAATATATTCTCTGTTGCT
genomic: GTCTTATCACTGGTGATGCTTCATCAAAAAGTAAAGCTGATAAAACCACTgtaagtaatc ... ctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCT
EST: gi|32850563|gb|CD990244.1|CD990244
EST:     AAAGTAAAGTTAATAAACCCACT                         GACCGTAAGAATGCAAGACAAGGGGAGACCATAAATATATTCCCTGTTGCT
genomic: AAAGTAAAGCTGATAAAACCACTgtaagtaatc ... ctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCT
EST: gi|32835266|gb|CD974944.1|CD974944
EST:     ATCACTGGTGATGCTTCATCAAAAAGTAAAGCTGATAAAACCACT                         GACCGTAAGGATGCAAGACAAGGGGAGACCATAAATATATTCTCTGTTGCT
genomic: ATCACTGGTGATGCTTCATCAAAAAGTAAAGCTGATAAAACCACTgtaagtaatc ... ctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCT
EST: gi|32850558|gb|CD990239.1|CD990239
EST:     TCAAAAAGTAAAGCTGATAAAACCCCT                         GACCGTAAGGATGCAAGCCAAGGGGAGACCATAAATATATTCCCTGTTGCC
genomic: TCAAAAAGTAAAGCTGATAAAACCACTgtaagtaatc ... ctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCT
EST: gi|32932543|gb|CF037355.1|CF037355
EST:     GTCTTATCACTGGTGATGCTTCATCAAAAAGTAAAGCTGATAAAACCACT                         GACCGTAAGGATGCAAGACAAGGGGAGACCATAAATATATTCTCTGTTGCT
genomic: GTCTTATCACTGGTGATGCTTCATCAAAAAGTAAAGCTGATAAAACCACTgtaagtaatc ... ctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCT
EST: gi|32850631|gb|CD990312.1|CD990312
EST:     AAAAGTAAAGCTGATAAAACCACT                         GACCGTAAGGATGCAAGCCAAGGGGAGACCATAAATATATTCCCTGTTGCT
genomic: AAAAGTAAAGCTGATAAAACCACTgtaagtaatc ... ctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCT
EST: gi|9743043|gb|BE519191.1|BE519191
EST:     GTCTTATCACTGGTGATGCTTCATCAAAAAGTAAAGCTGATAAAACCACT                         GACCGTAAGGATGCAAGACAAGGGGAGACCATAAATATATTCTCTGTTGCT
genomic: GTCTTATCACTGGTGATGCTTCATCAAAAAGTAAAGCTGATAAAACCACTgtaagtaatc ... ctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaacatttggggcatagaggaataccttacaagttttctatatctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCTTCTGGGCATCT
                         accttac  putative branch site (score: 3)
                                   ttttctatatcttt  putative PPT
                                   ttttctatatctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacttaatatagttccttggatgcatgtataatttatgactattttcaacatttggggcatagaggaataccttacaagttttctatatctttattcagGACCGTAAGGATGCAAGACAAGGGGAAACCATAAATATATTCTCTGTTGCTTCTGGGCATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - -acatttg