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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatggttacagttgaaacgtagttgatgacaaacagtcagtttacaagtatctgttgcccaatcgtatcgatctgcttaccaaattctcatgtttgcagGTTCCTTTGGAAGATGAGAAGAGGTTCAGGATTGAAATGACGTTCAGTCGTGGCGCCGATCTCAGTCCCCTAGAG

Basic information

species Zea mays
transcript GRMZM2G022997_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022997_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 28
tcatggttacagttgaaacgtagttgatgacaaacagtc---agtttacaagtatctgttgcccaatcgtatcgatctgcttaccaaattctcatgtttgcagGTTCCTTTGGAAGATGAGAAGAGGTTCAGGATTGAAATGACGTTCAGTCGTGGCGCCGATCTCAGTCCCCTAGAG
   |  |||| ||||  |    ||| |   | |    ||   | |||  | ||   ||||   || | || |  || ||||||||  ||| || | ||| ||||||||||| ||||||||||| |||||| ||||||||||||| || |||||||| || ||||| ||||| ||||||
cagttcttactgttgggataacgtttacagccagttctctggaatttggatgttgttgttttaca-tggtctt-atttgcttaccggatt-tcgtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG
















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|211369658|gb|FL316930.1|FL316930
EST:     AGCTTGATTACATGAGTAATATTGTGCTTAGAATGTTTGAAAACATAGAG                         GTTCCTTTGGAAGATGAGAAGAGGTTCAGGATTGAAATGACGTTCAGTCGT
genomic: AGCTTGATTACATGAGTAATATTGTGCTTAGAATGTTTGAAAACATAGAGgtatggatct ... atgtttgcagGTTCCTTTGGAAGATGAGAAGAGGTTCAGGATTGAAATGACGTTCAGTCGT
EST: gi|40286921|gb|CK327313.1|CK327313
EST:     AGCTTGATTACATGAGTAATATTGTGCTTAGAATGTTTGAAAACATAGAG                         GTTCCTTTGGAAGATGAGAAGAGGTTCAGGATTGAAATGACGTTCAGTCGT
genomic: AGCTTGATTACATGAGTAATATTGTGCTTAGAATGTTTGAAAACATAGAGgtatggatct ... atgtttgcagGTTCCTTTGGAAGATGAGAAGAGGTTCAGGATTGAAATGACGTTCAGTCGT
EST: gi|211101728|gb|FL471161.1|FL471161
EST:     AGCTTGATTACATGAGTAATATTGTGCTTAGAATGTTTGAAAACATAGAG                         GTTCCTTTGGAAGATGAGAAGAGATTCAGGATTGAAATGACGTTCAGTCGT
genomic: AGCTTGATTACATGAGTAATATTGTGCTTAGAATGTTTGAAAACATAGAGgtatggatct ... atgtttgcagGTTCCTTTGGAAGATGAGAAGAGGTTCAGGATTGAAATGACGTTCAGTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtatctgttgcccaatcgtatcgatctgcttaccaaattctcatgtttgcagGTTCCTTTGGAAGATGAGAAGAGGTTCAGGATTGAAATGACGTTCAGTCGTGGCGCCGATCTCAGTCCCCTAGAG
                             tgcttac  putative branch site (score: 2)
                                        ttctcat  putative PPT
                                     aaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatggttacagttgaaacgtagttgatgacaaacagtcagtttacaagtatctgttgcccaatcgtatcgatctgcttaccaaattctcatgtttgcagGTTCCTTTGGAAGATGAGAAGAGGTTCAGGATTGAAATGACGTTCAGTCGTGGCGCCGATCTCAGTCCCCTAGAG

- - - - - - - - - - - gttgatg
- - - - - - - - - - - - - - -acaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - ctgttgc