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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccatatatgcatttgtgtcggtctcttgtgtagtgtaggatcgcatatgaattaccaaaccttacaagttacatttgtttccaaatcgtgcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCATCCTTTGGGTGCCGGAGACAAAGGGAAGAACTCTCGAGGAGATACAATG

Basic information

species Zea mays
transcript GRMZM2G098679_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098679_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 16
gtccatatatgcatttgtgtcggtctcttgtgtagtgtaggatcgcata-tgaattaccaaaccttacaagtta--catttgtttccaaatcgtgcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCATCCTTTGGGTGCCGGAGACAAAGGGAAGAACTCTCGAGGAGATACAATG
|||| ||| |  ||     ||  ||| ||    ||  ||  ||     | ||| |||||  |   || ||||||   ||||  ||  || |    |||| ||||||   | ||||||||| |||||||||||||||||||| || |||||  |||||||||| |||||||||||||||||||| ||||||||||| | 
gtccgtatttctataaaaatcc-tctgttaccaagaataaaattctgaactgatttacctga---taaaagttaaatattttattttaatttcaacagGAACATTTTTGTCCTACATGATTGTGAGTGCTTTCACTCTCGTGTTCGTCATATTTTGGGTGCCAGAGACAAAGGGAAGAACTCTGGAGGAGATACAGTT

upper sequence: GRMZM2G098679_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 16
------------------------gtccatatatgcatttgtgtcggtctctt-gtgtagtg----taggatcgcatatgaattaccaaaccttacaagttacatttgtttccaaatcgt--gcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCATCCTTTGGGTGCCGGAGACAAAGGGAAGAACTCTCGAGGAGATACAATG
                           | |   |||| | |  | | ||| || ||  || |    |||  | | ||    | || | ||||| ||   | |   |   |||  || | |   |||| || ||||  | ||||||| | |||||||||||||| ||||| || ||||||||||||||||| |||||||| |||||||||||||| |||||||||||
gtacatacttctacttctctgatctctctttcctgcagtggaattgttcttttcgttgagcgagactagagtagaattctgaatatccaacctgacgc-tcatgctatcttcttaaacatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG
















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|37375628|gb|CF624264.1|CF624264
EST:     CTTTGGAATAACAATGACAGCAAATTTGCTTCTGTCCTGGAGTGCTGCAG                         GTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCA
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGTCCTGGAGTGCTGCAGgtccatatat ... aatcgtgcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCA
EST: gi|211280254|gb|FL478194.1|FL478194
EST:     CTTTGGAATAACAATGACAGCAAATTTGCTTCTGTCCTGGAGTGCTGCAG                         GTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCA
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGTCCTGGAGTGCTGCAGgtccatatat ... aatcgtgcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCA
EST: gi|148953878|gb|EC899256.2|EC899256
EST:     CTTTGGAATAACAATGACAGCAAATTTGCTTCTTTCCTGGAGTGCTGCAG                         GTACATTTGCCTTTTACATGATGGGGAGGGCTTTCACTTTCGTTTTTGTCA
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGTCCTGGAGTGCTGCAGgtccatatat ... aatcgtgcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCA
EST: gi|60401580|gb|DN234387.1|DN234387
EST:     CTTTGGAATAACAATGACAGCAAATTTGCTTCTGTCCTGGAGTGCTGCAG                         GTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCA
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGTCCTGGAGTGCTGCAGgtccatatat ... aatcgtgcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCA
EST: gi|211084269|gb|FL474824.1|FL474824
EST:     CTTTGGAATAACAATGACAGCAAATTTGCTTCTGTCCTGGAGTGCTGCAG                         GTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCA
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGTCCTGGAGTGCTGCAGgtccatatat ... aatcgtgcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcgcatatgaattaccaaaccttacaagttacatttgtttccaaatcgtgcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCATCCTTTGGGTGCCGGAGACAAAGGGAAGAACTCTCGAGGAGATACAATG
                    accttac  putative branch site (score: 3)
      atatgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccatatatgcatttgtgtcggtctcttgtgtagtgtaggatcgcatatgaattaccaaaccttacaagttacatttgtttccaaatcgtgcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCATCCTTTGGGTGCCGGAGACAAAGGGAAGAACTCTCGAGGAGATACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT