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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCATTGCTGGATCGTTAGCTGGGAAGCCATCCGATGGACGCCTGGTAAATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAGgtgattaaaactgcccacctcctcctttttttttgggtagatctcccaagcattatgcccctttgtaaaaacctttgtccattgccagttccatgcagagtctgcaaaccattttcagtgccacatgcgatcttctcaccaaagaatagtttgataacttgttattttgtgtatctgcag

Basic information

species Zea mays
transcript GRMZM2G058004_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058004_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g44140.1 (Oryza sativa), 5'ss of exon 7
AAGCATTGCTGGATCGTTAGCTGGGAAGCCATCCGATGGACGCCTGGTAAATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAGgtgattaaaactgcccacctcctcctttttttttgggtagatctcccaagcattatgcccctttgtaaaaacctttgtccattgccagttccatgcagagtctgcaaaccattttcagtgccacatgcgatcttctcaccaaagaatagtttgataacttgttattttgtgtatctgcag
||||||||||||||| ||  |||||||||| |||||||||    |||||||||| ||||||||||||||||| || |||||||  ||||||||||||||||| |            ||    |   || ||| | ||||||||         |||||     || | |||    ||  ||||||  |  | |||  |  |||     |  |                                                                     
AAGCATTGCTGGATCATTGACTGGGAAGCCCTCCGATGGATATTTGGTAAATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttctgatgatactatttaaattatttcttggtagatcatgt-----ttatgaaa--ttattaaagttatta-ccattggaa--ttcat-tatggtccattgataa---------------------------------------------------------------------
















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|211111421|gb|FL330318.1|FL330318
EST:     TCTCCCAATGATGCTTCTGCAGCAG                         GTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
genomic: TCTCCCAATGATGCTTCTGCAGCAGgtgattaaaa ... gtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
EST: gi|211537605|gb|FL330672.1|FL330672
EST:     TCTCCCAATGATGCTTCTGCAGCAG                         GTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
genomic: TCTCCCAATGATGCTTCTGCAGCAGgtgattaaaa ... gtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
EST: gi|60355590|gb|DN222563.1|DN222563
EST:     ATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAG                         GTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
genomic: ATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAGgtgattaaaa ... gtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
EST: gi|211015026|gb|FL312925.1|FL312925
EST:     TCTCCCAATGATGCTTCTGCAGCAG                         GTTG-CAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
genomic: TCTCCCAATGATGCTTCTGCAGCAGgtgattaaaa ... gtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
EST: gi|211058625|gb|FL339132.1|FL339132
EST:     TCTCCCAATGATGCTTCTGCAGCAG                         GTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
genomic: TCTCCCAATGATGCTTCTGCAGCAGgtgattaaaa ... gtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
EST: gi|211126986|gb|FL461323.1|FL461323
EST:     TCTCCCAATGATGCTTCTGCAGCAG                         GTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
genomic: TCTCCCAATGATGCTTCTGCAGCAGgtgattaaaa ... gtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
EST: gi|78121648|gb|DV540032.1|DV540032
EST:     ATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAG                         GTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
genomic: ATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAGgtgattaaaa ... gtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
EST: gi|211514893|gb|FL335491.1|FL335491
EST:     TCTCCCAATGATGCTTCTGCAGCAG                         GTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
genomic: TCTCCCAATGATGCTTCTGCAGCAGgtgattaaaa ... gtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
EST: gi|74233775|gb|DT641689.1|DT641689
EST:     ATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAG                         GTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
genomic: ATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAGgtgattaaaa ... gtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
EST: gi|78125655|gb|DV544039.1|DV544039
EST:     ATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAG                         GTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG
genomic: ATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAGgtgattaaaa ... gtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCATTGCTGGATCGTTAGCTGGGAAGCCATCCGATGGACGCCTGGTAAATAGTTACAATTGTGACTTGGAAGATCTCCCAATGATGCTTCTGCAGCAGgtgattaaaactgcccacctcctcctttttttttgggtagatctcccaagcattatgcccctttgtaaaaacctttgtccattgccagttccatgcagagtctgcaaaccattttcagtgccacatgcgatcttctcaccaaagaatagtttgataacttgttattttgtgtatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG