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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcttgtttgctgtgattaaatccttgttttggtgctcttcctttgagaactaaacattatcttgtgtattctgcagCAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAAAGTACCAGAGATATTGGCAATTTGGAGAGACGACCTGAGTAAA

Basic information

species Zea mays
transcript GRMZM2G086015_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
------gtaaatcttgtttgctgtgattaaatccttgttttggtgctcttcctttgagaactaaacattatcttgtgtattctgcagCAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAAAGTACCAGAGATATTGGCAATTTGGAGAGACGACCTGAGTAAA
      ||| ||| |||||||||| || || |||   || | ||        ||| | | |||||| | ||||  |||||| | |||||| ||||||||||||||||| ||| |||| ||||| |||||||| ||||||||  | |||||| | ||||| |||||| | ||||| ||||||
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatct-atgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA

upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
------gtaaatcttgtttgctgtgattaaatccttgttttggtgctcttcctttgagaactaaacattatcttgtgtattctgcagCAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAAAGTACCAGAGATATTGGCAATTTGGAGAGACGACCTGAGTAAA------
      ||| ||| |||||||||| || || |||   || | ||        ||| | | |||||| | ||||  |||||| | |||||| ||||||||||||||||| ||| |||| ||||| |||||||| ||||||||  | |||||| | ||||| |||||| | ||||| ||||||      
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatct-atgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
















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|7216455|gb|AW562577.1|AW562577
EST:     CTTTTTATGCTTGGTAAAGTTGAAGATTGCATACAGTTGCTTGTAGACAG                         TAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAA
genomic: CTTTTTATGCTCGGTAAAGTTGAAGATTGCATACAGTTGCTTGTAGACAGgtaaatcttg ... tattctgcagCAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAA
EST: gi|160481598|gb|EY254430.1|EY254430
EST:     CTTTTTATGCTTGGTAAAGTTGAAGATTGCATACAGTTGCTTGTAGACAG                         TAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAA
genomic: CTTTTTATGCTCGGTAAAGTTGAAGATTGCATACAGTTGCTTGTAGACAGgtaaatcttg ... tattctgcagCAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAA
EST: gi|67024352|gb|CO453101.1|CO453101
EST:     CTTTTTATGCTTGGTAAAGTTGAAGATTGCATACAGTTGCTTGTAGACAG                         TAACCGTATACCTGAAGCTGCATTACTGGCTCGTTCATATCTTCCTAGCAA
genomic: CTTTTTATGCTCGGTAAAGTTGAAGATTGCATACAGTTGCTTGTAGACAGgtaaatcttg ... tattctgcagCAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgttttggtgctcttcctttgagaactaaacattatcttgtgtattctgcagCAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAAAGTACCAGAGATATTGGCAATTTGGAGAGACGACCTGAGTAAA
                          aactaaa  putative branch site (score: 2)
                             taaacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcttgtttgctgtgattaaatccttgttttggtgctcttcctttgagaactaaacattatcttgtgtattctgcagCAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAAAGTACCAGAGATATTGGCAATTTGGAGAGACGACCTGAGTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA