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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttttttcttgaacggaatacattagtttaatgattttgtgccttgtttcaatagagttttgttctgtacatttccagGGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCATGTCCTATTTATAACTGTGATGGAAG

Basic information

species Zea mays
transcript GRMZM2G011364_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011364_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g39650.1 (Oryza sativa), 3'ss of exon 5
------gtgagttttttttcttgaacggaatacattagtttaatgattttgtgccttgtttcaatagagttttgttctgt-acatttccagGGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCATGTCCTATTTATAACTGTGATGGAAG
       || || | |||   ||    ||| ||||  |||     ||| |||   |||||| ||  ||||||  | || | |||||||||||| ||||||||||| |||||||||||||||||| || |||||||||||||  |||| ||| | || | |||| |||
gtgagtatgtgtgtgtttatgtgttttgaaaacatatgttggtgtattgtgt---ttgttttaagtgagtttcttgctttcacatttccagGGAGAAATATTTGGTTTCTGCAGATTCTCTAATCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAG
















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|93284045|gb|EB676309.1|EB676309
EST:     TGTGGGATTTGCAGTCATCTGAAGTTGTAGCCAGTCTGCCAAGAGAAACA                         GGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCAT
genomic: TGTGGGATTTGCAGTCATCTGAAGTTGTAGCCAGTCTGCCAAGAGAAACAgtgagttttt ... acatttccagGGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCAT
EST: gi|32945451|gb|CF050270.1|CF050270
EST:     TGTGGGATTTGCAGTCATCTGAAGTTGTAGCCAGTCTGCCAAGACAAGCA                         GGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGTTGACAACAGTCAT
genomic: TGTGGGATTTGCAGTCATCTGAAGTTGTAGCCAGTCTGCCAAGAGAAACAgtgagttttt ... acatttccagGGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCAT
EST: gi|6020933|gb|AW065861.1|AW065861
EST:     GCCAGTCTGCCAAGAGAAACA                         GGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCAT
genomic: GCCAGTCTGCCAAGAGAAACAgtgagttttt ... acatttccagGGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCAT
EST: gi|32827142|gb|CD966820.1|CD966820
EST:     TGTGGGATTTGCAGTCATCTGAAGTTGTAGCCAGTCTGCCAAGACAAACA                         GGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGTTGACAACAGTCAT
genomic: TGTGGGATTTGCAGTCATCTGAAGTTGTAGCCAGTCTGCCAAGAGAAACAgtgagttttt ... acatttccagGGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCAT
EST: gi|78083929|gb|DV512322.1|DV512322
EST:     TGTGGGATTTGCAGTCATCTGAAGTTGTAGCCAGTCTGCCAAGAGAAACA                         GGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCAT
genomic: TGTGGGATTTGCAGTCATCTGAAGTTGTAGCCAGTCTGCCAAGAGAAACAgtgagttttt ... acatttccagGGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttaatgattttgtgccttgtttcaatagagttttgttctgtacatttccagGGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCATGTCCTATTTATAACTGTGATGGAAG
  gtttaat  putative branch site (score: 4)
                                              catttcc  putative PPT
     taatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttttttcttgaacggaatacattagtttaatgattttgtgccttgtttcaatagagttttgttctgtacatttccagGGGGAAATATTTGGATTCTGCAGATTCTCTAATAAGGCTGACAACAGTCATGTCCTATTTATAACTGTGATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG