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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaggaaagattaagccaccttagaacaggcaagcttctctttgttggccctctattctgaattctgaacttatttcttgggttgccactaatgtgcagGATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGTGTTGAACAG

Basic information

species Zea mays
transcript GRMZM2G052479_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052479_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g17600.1 (Oryza sativa), 3'ss of exon 3
atgaggaaagattaagccaccttagaacaggcaagcttctctttgt-tggccctctattctgaattctgaacttatttcttgggtt-gccactaatgtgcagGATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGTGTTGAACAG
  |  | ||  | |        |  | |   | ||||| || |  | |     |  | |||   |  |  |  || |  || | ||  ||||| |  | |||||||  ||| | ||||| || ||||||||||||||||| |||||||||| ||||||||||
--gttgcaaattcattagtttctgtagctttcgagcttttcataatattatgttgaactctttttcgtccatctaatctttagtttcaccacttacattcagGATGCAATGGAGGCTGCAGGGGTTGCTCTTGTTTTAATCGGACCAGGTACTGTTGAACAG
















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|94472720|gb|EB701678.1|EB701678
EST:     TCGGGTGCGTGCTGTGCCGAAAGAGGGCGGACTTTCTCTCCGCGAAACAG                         GATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGT
genomic: TCGGGTGCGTGCTGTGCCGAAAGAGGGCGGACCTTCTCGCCGCGAAACAGgttcctagct ... taatgtgcagGATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGT
EST: gi|93012301|gb|EB637821.1|EB637821
EST:     GTGCGTGCTGTGCCGAAAGAGGGCGGACCTTCTCGCCGCGAAACAG                         GATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTTATTGGACCAGGTAGT
genomic: GTGCGTGCTGTGCCGAAAGAGGGCGGACCTTCTCGCCGCGAAACAGgttcctagct ... taatgtgcagGATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGT
EST: gi|211321654|gb|FL407918.1|FL407918
EST:     GTGCGTGCTGTGCCGAAAGAGGGCGGACCTTCTCGTCGCGAAACAG                         GATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGT
genomic: GTGCGTGCTGTGCCGAAAGAGGGCGGACCTTCTCGCCGCGAAACAGgttcctagct ... taatgtgcagGATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGT
EST: gi|211373863|gb|FL386282.1|FL386282
EST:     GTGCGTGCTGTGCCGAAAGAGGGCGGACCTTCTCGTCGCGAAACAG                         GATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGT
genomic: GTGCGTGCTGTGCCGAAAGAGGGCGGACCTTCTCGCCGCGAAACAGgttcctagct ... taatgtgcagGATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGT
EST: gi|101386886|gb|EB815460.1|EB815460
EST:     GTGCGTGCTGTGCCGAAAGAGGGCGGACCTTCTCGCCGCGAAACAG                         GATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGT
genomic: GTGCGTGCTGTGCCGAAAGAGGGCGGACCTTCTCGCCGCGAAACAGgttcctagct ... taatgtgcagGATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggccctctattctgaattctgaacttatttcttgggttgccactaatgtgcagGATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGTGTTGAACAG
                                          cactaat  putative branch site (score: 2)
                       aacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaggaaagattaagccaccttagaacaggcaagcttctctttgttggccctctattctgaattctgaacttatttcttgggttgccactaatgtgcagGATGACATGCAAGCTGCTGGAGTTGCTCTTGTTTTAATTGGACCAGGTAGTGTTGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA