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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttccttgtccctttcctgaagtgtgatgcatattattatttatgtttcctctattgttctctgactgctcgtgtggttattatttatgtttctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGTCCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCCACAG

Basic information

species Zea mays
transcript GRMZM2G060284_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060284_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 3'ss of exon 5
---------------------------------------------gtatttccttgtccctttcctgaagtgtgatgcatattattatttatgtttcctctattgttctctgactgctcgtgtggttattatttatgtttc--tctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGTCCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCCACAG
                                               |||   |       ||  |     ||| | |     |  |   || |||  |  |||  ||||  | || | |  | || ||| ||| || |||  | ||||||||||||||||||||||||  |||| ||||||||| | || || |||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||
gtatattcttgatttatttggcgtctctatttttaagtgaaaaaaacattggttaagatactttatttgtggtgttcctatgaacaacaaatattttattcattactctc--aatggttgctttgtgattgtttgtgcttcgttttatgcagCAATTCCTGAAGGAGATTCTGAATGATCTGTGTTTTTACAACAAACGAGGACCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCTACAG

upper sequence: GRMZM2G060284_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G03070.1 (Glycine max), 3'ss of exon 5
gtatttccttgtccctttcctgaagtgtgatgcatattattatttatgtttcctctattgttctctgactgctcgtgtggttattatttatgtttctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGTCCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCCACAG
  | | ||| |   |  |||            |    | ||  ||    || |   | |  | |   |  | || ||     | |  | |  |||   |  |||||||||| |||| |||||  ||||||| || ||||| || |||||| ||||| | || || |||||  | ||||| ||||||||||||||||||||    |
-cactgcctggcggccatcccctcacactccacccccttttcctt----ttgcagcaattctttgaaaaagatcctgaatgaacttgtgaccttttctttcgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACTTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG

upper sequence: GRMZM2G060284_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G03030.1 (Glycine max), 3'ss of exon 5
gtatttccttgtccctttcctgaagtgtgatgcatattattatttatgtttcctctattgttctctgactgctcgtgtggttattatttatgtttctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGTCCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCCACAG
     ||  || || |   |         |  |  |      ||| | |||         || |   |  | || ||     | |  | |  |||   | ||||||||||| |||| |||||  ||||||| || ||||| || |||||| ||||| | || || |||||  | ||||| ||||||||||||||||||||    |
-----tcactgcccgtcggccatccccatacactcagccccctttttcttttgcagcaatttttaaaaaagatcctgaatgaactcgtgactttttcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACCTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG

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|33467249|gb|CF244298.1|CF244298
EST:     GACCAGCCAGAG                         CAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
genomic: GACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
EST: gi|13515926|gb|BG518202.1|BG518202
EST:     AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAG                         CAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
genomic: AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
EST: gi|94479553|gb|EB708511.1|EB708511
EST:     AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAG                         CAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
genomic: AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
EST: gi|149085564|gb|EE175076.2|EE175076
EST:     AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAG                         CAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
genomic: AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
EST: gi|50324691|gb|CO519817.1|CO519817
EST:     AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAG                         CAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
genomic: AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
EST: gi|94479552|gb|EB708510.1|EB708510
EST:     AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAG                         CAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
genomic: AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
EST: gi|211224212|gb|FK968311.1|FK968311
EST:     AGCCCAATTGGGCCCTAAAGGCCCTCGTGCAAGAAACTGACCAGCCAGAG                         CAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGA
genomic: AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
EST: gi|149085565|gb|EE175077.2|EE175077
EST:     AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAG-AGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
genomic: AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
EST: gi|13490745|gb|BG517509.1|BG517509
EST:     AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAG                         CAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGG
genomic: AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
EST: gi|76937460|gb|DV175147.1|DV175147
EST:     AGCCCAATTGGGTCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAG                         CAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
genomic: AGCCCAATTGGGCCCTAAAGGCACTCGTGCAAGAAACTGACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
EST: gi|32867817|gb|CF007499.1|CF007499
EST:     TCGTGCAAGAAACTGACCAGCCAGAG                         CAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT
genomic: TCGTGCAAGAAACTGACCAGCCAGAGgtatttcctt ... ctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctctattgttctctgactgctcgtgtggttattatttatgtttctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGTCCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCCACAG
            ctctgac  putative branch site (score: 3)
                                        tgtttctct  putative PPT
                              ttattatttatgtttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttccttgtccctttcctgaagtgtgatgcatattattatttatgtttcctctattgttctctgactgctcgtgtggttattatttatgtttctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGTCCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA