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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacacatatatgctttttcagctgaatcgagatgaaactgaattttgcgatacacaagaccacctaatacatgtctctatgaaactgtgccggcgcaataatgcag

Basic information

species Zea mays
transcript GRMZM2G005859_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005859_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g01014.1 (Oryza sativa), 5'ss of exon 5
GGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacacatatatgctttttcagctgaatcgagatgaaa-ctgaattttgcgatacacaagaccacctaatacatgtctctatgaaactgtgccggcgcaataatgcag
|| || ||||| |||||||| |||||| |||| ||||| ||||| || ||||||||||||||||| ||||||| ||  | ||  ||||||  ||| |  || || ||| |  |   | |||| ||||     |   | ||  ||  |||    ||  |  ||||  |              
GGTGCGTTGGCTGATATTTTTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTGgtatgaattc-tac-tgcttt--cagttcgatggaaatggagtcctgaatttgggatatttgcgctgatct--taactgtgctgattgatatgtgtag--------------
















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|9028720|gb|BE238760.1|BE238760
EST:     TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG                         AGTGGTATCGTTCCTCCTCTGGTTCCATTCGCTCAGACGTTCGCGGCAGTC
genomic: TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacac ... aataatgcagAGTGGTATCGTTCCTCCTCTGGTTCCATTCGCTCAGACGTTCGCGGCAGTC
EST: gi|211010141|gb|FL113888.1|FL113888
EST:     TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG                         AAGTGGTATCG
genomic: TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacac ... aataatgcagA-GTGGTATCG
EST: gi|71445181|gb|DR826231.1|DR826231
EST:     TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG                         AGTGGTATCGTTCCTCCTCTGGTTCCATTCGCTCAGACGGTCGCGGCAGTC
genomic: TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacac ... aataatgcagAGTGGTATCGTTCCTCCTCTGGTTCCATTCGCTCAGACGTTCGCGGCAGTC
EST: gi|9953868|gb|BE640451.1|BE640451
EST:     TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG                         AGTGGTATCGTTCCTCCTCTGGTTCCATTCGCTCAGACGTTCGCGGCAGTC
genomic: TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacac ... aataatgcagAGTGGTATCGTTCCTCCTCTGGTTCCATTCGCTCAGACGTTCGCGGCAGTC
EST: gi|9028504|gb|BE238499.1|BE238499
EST:     TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG                         AGTGGTATCGTTCCTCCTCTGGTTCCATTCGCTCAGACGTTCGCGGCAGTC
genomic: TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacac ... aataatgcagAGTGGTATCGTTCCTCCTCTGGTTCCATTCGCTCAGACGTTCGCGGCAGTC
EST: gi|76290855|gb|DV030423.1|DV030423
EST:     TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG                         AGTGGTATCGTTCCTCCTCTGGGTTC-ATTCGCTCAGACGTTCGCGGCAGT
genomic: TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacac ... aataatgcagAGTGGTATCGTTCCTCCTCTGG-TTCCATTCGCTCAGACGTTCGCGGCAGT
EST: gi|78091085|gb|DV519459.1|DV519459
EST:     TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG                         AGTGGTATCGTTCCTCCTCTGGNTTC-ATTCGCTCAGACGTTCGCGGCAGT
genomic: TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacac ... aataatgcagAGTGGTATCGTTCCTCCTCTGG-TTCCATTCGCTCAGACGTTCGCGGCAGT
EST: gi|13149629|gb|BG319951.1|BG319951
EST:     TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG                         AGTGGTATCGTTCCTCCTCTGGTTCCATTCGCTCAGACGTTCGCGGCAGTC
genomic: TCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacac ... aataatgcagAGTGGTATCGTTCCTCCTCTGGTTCCATTCGCTCAGACGTTCGCGGCAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTGgtataaacacatatatgctttttcagctgaatcgagatgaaactgaattttgcgatacacaagaccacctaatacatgtctctatgaaactgtgccggcgcaataatgcag

- - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - -  AGGATG