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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGCGACGGAACTGCTCGAGATAAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgccgccacgcttatagtcgaagcaagggagaggattggtaatgttcatgcactcttgaatgaaactagtttctgttctgttctgtag

Basic information

species Zea mays
transcript GRMZM2G133959_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133959_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g72870.1 (Oryza sativa), 5'ss of exon 4
CTTTGCGACGGAACTGCTCGAGATAAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgccgccacgcttatagtcgaagcaagggagaggattggtaatgttcatgcactcttgaatgaaactagtttctgttctgttctgtag
||||||||||||  | |||||||||||| |||||||||||||  | || || ||| ||||| | || || ||||||  |||   | |      |      |||   | |    | |||| | |||     | | |   |         | |     | |||||  | ||
CTTTGCGACGGATTTTCTCGAGATAAGGGCCAAAGAGCCGTCTGTTCATGTTCTGGTTATTCCCGGAAATCCAGgttagtggcacactgaagatcggtgagaattgatgtgttgcattgctcatgaaagagtattgaggtcattggagaatcctgttgctgtttggcag
















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|50336059|gb|CO531185.1|CO531185
EST:     AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAG                         GCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACC
genomic: AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACC
EST: gi|211452694|gb|FL421169.1|FL421169
EST:     AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACC-AG                         GNATCGCTGCGTTTTATAAGGACTG
genomic: AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTG
EST: gi|149081438|gb|EE170561.2|EE170561
EST:     AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAG                         GCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
genomic: AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
EST: gi|211501850|gb|FL388433.1|FL388433
EST:     GGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAAACCCAG
genomic: GGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAA-CCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGCGACGGAACTGCTCGAGATAAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgccgccacgcttatagtcgaagcaagggagaggattggtaatgttcatgcactcttgaatgaaactagtttctgttctgttctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT