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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtatgctgcatttttcatactcatagttgtcaagtaatttgcagagtggtggcatgctgaatctgaattttgaataaccagGTACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGGCTTGCTGCTATAGCCTGGCATGATGAACTCGCCCCTTTGCCTAAGCCGTTGC

Basic information

species Zea mays
transcript GRMZM2G026900_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026900_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g33230.1 (Oryza sativa), 3'ss of exon 4
--gtggtatgctgcatttttcatactcatagttgtcaagtaatttgcagagtggtggcatgctgaatctgaattttgaataa--ccagGTACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGGCTTGCTGCTATAGCCTGGCATGATGAACTCGCCCCTTTGCCTAAGCCGTTGC
   || |    |   || || ||  |   |  ||  || |  || |||  | | || ||| || | |||| |||||||| ||   ||||| ||||||||||||||||||||||| |||||||||||||| || || ||||||||||||||||||||||||||||||||||||||||||||||| ||||
gtatgctgctttctcttctttattttgggaagtgaaaaatggtt-gcactgcgatgtcatacttattctggattttgaaaaagttcagGTGCTTACTGTTGGTGCACTACACCAAGCTGATTCTGCTGCACTGCGCCTTGCTGCTATAGCCTGGCATGATGAACTCGCCCCTTTGCCTAAGCCATTGC
















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|89759150|gb|DY688059.1|DY688059
EST:     CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAAT                         GTGGTACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGG
genomic: CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAATgtggtatgct ... gaataaccagGT---ACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGG
EST: gi|76014611|gb|DT941781.1|DT941781
EST:     CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAAT                         GTACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGGCTT
genomic: CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAATgtggtatgct ... gaataaccagGTACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGGCTT
EST: gi|148932641|gb|EC876549.2|EC876549
EST:     CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAAT                         GTGGTACTTACTGTTGGTGCACTACACCAGGC
genomic: CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAATgtggtatgct ... gaataaccagGT---ACTTACTGTTGGTGCACTACACCAGGC
EST: gi|149059442|gb|EE156927.2|EE156927
EST:     CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAAT                         GTGGTACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGG
genomic: CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAATgtggtatgct ... gaataaccagGT---ACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGG
EST: gi|71329061|gb|DR801238.1|DR801238
EST:     CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAAT                         GTGGTACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGG
genomic: CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAATgtggtatgct ... gaataaccagGT---ACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGG
EST: gi|148942515|gb|EC887530.2|EC887530
EST:     CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTATT                         GTGGTACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCT
genomic: CACACCTGTTCCGCAGATGGATTACTCCACAGGAACCACCCAGGAGTAATgtggtatgct ... gaataaccagGT---ACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcaagtaatttgcagagtggtggcatgctgaatctgaattttgaataaccagGTACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGGCTTGCTGCTATAGCCTGGCATGATGAACTCGCCCCTTTGCCTAAGCCGTTGC
                                     tgaattttgaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtatgctgcatttttcatactcatagttgtcaagtaatttgcagagtggtggcatgctgaatctgaattttgaataaccagGTACTTACTGTTGGTGCACTACACCAGGCTGATTCTGCTGCGCTACGGCTTGCTGCTATAGCCTGGCATGATGAACTCGCCCCTTTGCCTAAGCCGTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT