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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttcacttcaattacgatgttttgttttgttagtgtgggctggagttgagattagtgctgcacagaccattcttaaacgactctctgcatctatgcagGCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGGTTGAAGATCTTTTCTCCGAATGTCCTTAACATTACTTTAGTCG

Basic information

species Zea mays
transcript GRMZM2G129155_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 1
tgtttcacttcaattacgatgttttgttttgttagtgtgggctggagttgag--attagtgct-----gcacagaccattcttaaacgactctctgcatctatgcagGCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGGTTGAAGATCTTTTCTCCGAATGTCCTTAACATTACTTTAGTCG
      | ||    |    ||||| ||| ||  | ||   ||  | |||||   |   || |      ||| ||| || | |||| | | || |   ||| |||||||| ||||||||  | ||||| ||||||||||||||||| || |||| |||||||||  |||||||||  || || ||||| || |||||||| || || |
------agttatgctggtttgtttagttatgccaatgcctgcaagtgttgaacaaactgtaccatagggcatagagcactattaatc-attcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG

upper sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 1
--tgtttcacttcaattacgatgttttgttttgttagtgtgggctggagttgagattagtgctgcacagaccattcttaaacgactctctgcatctatgcagGCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGGTTGAAGATCTTTTCTCCGAATGTCCTTAACATTACTTTAGTCG
  |||   |||     | |    || | |   ||     ||               ||   ||     ||| | | |  | |  | |||    | | ||||||||||||| ||| | || |||||||| ||||||||||| || || | |||||| ||  ||||||| ||||| || ||||| ||| | || || || || |
aatgtaatactcttgatgccgatttgtatacggtctacttgtttaatcccccctcctatctctctgttgactagtat--atcttcactcactttttctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
















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|149075510|gb|EE164038.2|EE164038
EST:     TCTCGGGGCGTCGCTTCTACGACTTCCGCGAAATCCGACGCGAGATCCAG                         GCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAG
genomic: TCTCGGGGCGTCGCTTCTACGACTTCCGCGAAATCCGACGCGAGATCCAGgtccccatcc ... atctatgcagGCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAG
EST: gi|91874420|gb|EB404377.1|EB404377
EST:     TCTCGGGGCGTCGCTTCTACGACTTCCGCGAAATCCGACGCGAGATCCAG                         GCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAG
genomic: TCTCGGGGCGTCGCTTCTACGACTTCCGCGAAATCCGACGCGAGATCCAGgtccccatcc ... atctatgcagGCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAG
EST: gi|91874421|gb|EB404378.1|EB404378
EST:     TCTCGGGGCGTCGCTT-TACGATTTCCGCGAAATCCGCCGCGAGATCCAG                         GCTGAACCAGTTCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAG
genomic: TCTCGGGGCGTCGCTTCTACGACTTCCGCGAAATCCGACGCGAGATCCAGgtccccatcc ... atctatgcagGCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgagattagtgctgcacagaccattcttaaacgactctctgcatctatgcagGCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGGTTGAAGATCTTTTCTCCGAATGTCCTTAACATTACTTTAGTCG
                         attcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttcacttcaattacgatgttttgttttgttagtgtgggctggagttgagattagtgctgcacagaccattcttaaacgactctctgcatctatgcagGCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGGTTGAAGATCTTTTCTCCGAATGTCCTTAACATTACTTTAGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA