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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttgtatttgttgacactgataggaaacataaatagctatgttccaaggagctggctgataaatctagtctttgtgatatgtcttacaagtatatcagTTTAATGTTTGCAGGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGTTGAGCATGTGGATAAGGACAATGATGGTATTATTACTTTTGAGGAGTGG

Basic information

species Zea mays
transcript GRMZM2G180971_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180971_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g10740.1 (Oryza sativa), 3'ss of exon 1
gtgttgtatttgttgacactgataggaaacataaatagctatgttccaaggagctggctgataaatctagtctttgtgatatgtcttacaagta-tatcagTTTAATGTTTGCAGGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGTTGAGCATGTGGATAAGGACAATGATGGTATTATTACTTTTGAGGAGTGG--------------
         || ||  | ||  ||       |||||  |||||| | | | |     ||||||| | ||||| || ||||  |||||||||||| |||||||||  |||||||||| |||||||||||||| || ||||||||||||||||||||||||||||||||||| ||| |||| |||||||||||||| || |||              
-------ggtttttttccctattat------taaatcactatgtcctaggaaagcacctgataattgtagtccttttgat--gtcttacaagtaatatcagtttgctgtttgcagGCATAGAAATTGATGACGAGGAGCTTGCAAGATTTGTTGAGCATGTGGATAAGGATAATAATGGAATTATTACTTTTGAAGAATGGAGGGACTTTCTTTT

upper sequence: GRMZM2G180971_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0068g00890.t01 (Vitis vinifera), 3'ss of exon 1
gtgttgtatttgttgacactgataggaaacat-aaatagctatgttccaaggagctggctgataaatctagtctttgtgatatgtcttacaagt-atatcagTTTAATGTTTGCAGGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGTTGAGCATGTGGATAAGGACAATGATGGTATTATTACTTTTGAGGAGTGG--------------
                  || |||   | | | |||  |   | |||  ||    ||| |   || | |||    |    |   || || |||    | |||| |    |||| ||| ||  ||||||||||||| ||||||||  |||||||||| | |||||| ||||| ||| ||||  | || || ||||| || |||              
---------------ttgcttatatatacctttaaacggaattcttctcagagaatggttc-caattttagctggtcattttcatcctataagccgcagcagtctctcttttgtagGGATTAAAATTGATGATGAGGAGCTTGCTCGATTTGTTGAACGTGTGGACAAGGATAATAATGGGGTCATAACATTTGAAGAATGGAGAGATTTTCTTTT
















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|148991808|gb|EE033391.2|EE033391
EST:     CAACGGATGTATCCTGCCCGAGGAGCTCTGGCACGCGCTCGTCCAGGCTG                         TTTAATGTTTGCAGGTATAGAAATTGATGATGAAGAGCTTGCCAGATTTGT
genomic: CAACGGATGTATCCTGCCCGAGGAGCTCTGGCACGCGCTCGTCAAGGCTGgtaactgcaa ... agtatatcagTTTAATGTTTGCAGGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGT
EST: gi|71323061|gb|DR798204.1|DR798204
EST:     CAACGGATGTATCCTGCCCGAGGAGCTCTGGCACGCGCTCGTCAAGGC--                         ---------T---GGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGT
genomic: CAACGGATGTATCCTGCCCGAGGAGCTCTGGCACGCGCTCGTCAAGGCTGgtaactgcaa ... agtatatcagTTTAATGTTTGCAGGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGT
EST: gi|148941387|gb|EC886303.2|EC886303
EST:     CAACGGATGTATCCTGCCCGAGGAGCTCTGGCACGCGCTCGTCAAGGCTG                         ------GT----A--TA--GAAATTGATGATGAAGAGCTTGCAAGATTTGT
genomic: CAACGGATGTATCCTGCCCGAGGAGCTCTGGCACGCGCTCGTCAAGGCTGgtaactgcaa ... agtatatcagTTTAATGTTTGCAGGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGT
EST: gi|148940839|gb|EC885670.2|EC885670
EST:     CAACGGATGTATCCTGCCCGAGGAGCTCTGGCACGCGCTCGTCAAGGCTG                         ------GT----A--TA--GAAATTGATGATGAAGAGCTTGCAAGATTTGT
genomic: CAACGGATGTATCCTGCCCGAGGAGCTCTGGCACGCGCTCGTCAAGGCTGgtaactgcaa ... agtatatcagTTTAATGTTTGCAGGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaggagctggctgataaatctagtctttgtgatatgtcttacaagtatatcagTTTAATGTTTGCAGGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGTTGAGCATGTGGATAAGGACAATGATGGTATTATTACTTTTGAGGAGTGG
                                     gtcttac  putative branch site (score: 3)
               ataaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttgtatttgttgacactgataggaaacataaatagctatgttccaaggagctggctgataaatctagtctttgtgatatgtcttacaagtatatcagTTTAATGTTTGCAGGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGTTGAGCATGTGGATAAGGACAATGATGGTATTATTACTTTTGAGGAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
-tgttgta
- - - - tttgttg
- - - - - - - - - - - - - aaacata
- - - - - - - - - - - - - - - - - - - - - - - - -ggagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgata