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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcggtctggtgcaagtggcaatcagatattaaaattctactattacgatttgatgttcacttagctttatcatattcatgttgatttgataaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGCTGTGGCTGTGGCACTCTGGCTGTGGCGAGTGCTTTACTGGATGCTGA

Basic information

species Zea mays
transcript GRMZM2G113640_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113640_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g06730.1 (Oryza sativa), 3'ss of exon 2
------tcggt--ctggtgcaagtggcaatcagatattaaaattctactattacgatttgatgttcacttagctttatcatattcatgttgatttgataaata-atcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGCTGTGGCTGTGGCACTCTGGCTGTGGCGAGTGCTTTACTGGATGCTGA
      | | |  ||||     | |    ||||||  ||| |||| | |     | | || |||   |||   ||||||    ||||  |||||  ||||||  ||||||| |||||||||||  |||||||||||||||||||||| |||||||| ||||| || |||||||| ||| ||||||| ||  || | |||||||||||
aaatagtagatggctggcatgtgcgctgttcagatgctaacattcaagt----tgttctggtgt--gctt---tttatctcgctcatagtgattccataaatccatcagGCGGAGAATAGTTTTGATGACATAACTGGCAAAGTGGTGGCTGACTTTGGCTGCGGGTGTGGCACCCTGTCTGTGGCAAGCTCTCTGCTGGATGCTGA
















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|211270646|gb|FL248436.1|FL248436
EST:     TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG                         GCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
genomic: TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATGgttagtgctg ... aaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
EST: gi|211270652|gb|FL248442.1|FL248442
EST:     TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG                         GCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
genomic: TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATGgttagtgctg ... aaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
EST: gi|211270657|gb|FL248447.1|FL248447
EST:     TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG                         GCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
genomic: TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATGgttagtgctg ... aaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
EST: gi|211270648|gb|FL248438.1|FL248438
EST:     TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG                         GCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
genomic: TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATGgttagtgctg ... aaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
EST: gi|211270651|gb|FL248441.1|FL248441
EST:     GGAGCAGTATGCR-CGGGGCCCTCACATCGCGTCGCGGATGCTCTACATG                         GCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
genomic: GGAGCAGTATGCGACGGG-CCCTCACATCGCGTCGCGGATGCTCTACATGgttagtgctg ... aaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
EST: gi|211270649|gb|FL248439.1|FL248439
EST:     TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG                         GCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
genomic: TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATGgttagtgctg ... aaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
EST: gi|211270655|gb|FL248445.1|FL248445
EST:     TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG                         GCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
genomic: TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATGgttagtgctg ... aaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
EST: gi|211270656|gb|FL248446.1|FL248446
EST:     TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG                         GCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
genomic: TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATGgttagtgctg ... aaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGC
EST: gi|211050250|gb|FL241531.1|FL241531
EST:     TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG                         GCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGTCTAGCTG
genomic: TGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATGgttagtgctg ... aaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTG---A-CT-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatttgatgttcacttagctttatcatattcatgttgatttgataaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGCTGTGGCTGTGGCACTCTGGCTGTGGCGAGTGCTTTACTGGATGCTGA
                                   ttgatttgataaataa  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcggtctggtgcaagtggcaatcagatattaaaattctactattacgatttgatgttcacttagctttatcatattcatgttgatttgataaataatcagGCAGAGAATAGTTTCAATGACATAACTGGCAAAGTGGTAGCTGACTTCGGCTGTGGCTGTGGCACTCTGGCTGTGGCGAGTGCTTTACTGGATGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG