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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtatatcaaacttctttctattcgttttgttcctgtatttgacttgatcatattgacatttggactttggctcggtttttttatgagcaattcga...

Basic information

species Zea mays
transcript GRMZM2G171406_T05
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171406_T06 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os10g40140.1 (Oryza sativa), 5'ss of exon 8
ATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtatatcaaacttctttcta----ttcgttttgttcc-tgtatttgacttgatcatattgacatttggactttggctcggtttttttatgagcaattcga
|| |||||||| || ||  | ||||| ||| |||||| ||  || |||||||||||||||||||||||||||||||| |||  | |     |||||| |     ||| |||||||   ||    | |||| ||   ||||    ||  |  ||  |||  | ||   |   | | |    
ATACAGACAATACAACGCCTAAAAGACGAACGAGACACCACCCTGCAGCAAAATCAGCAAATGCAACGTGAATTGgt-cagccttttttttttcttttttgcacttcattttgttttgtgatcatcactttatttcattgtagcttttatgttt-ctcaatattgacacctgaactg---
















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|94475041|gb|EB703999.1|EB703999
EST:     AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG                         GATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
genomic: AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtata ... ctgtgttcagGATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
EST: gi|16919153|gb|BM074062.1|BM074062
EST:     AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG                         GATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
genomic: AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtata ... ctgtgttcagGATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
EST: gi|60397188|gb|DN230004.1|DN230004
EST:     AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG                         GATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
genomic: AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtata ... ctgtgttcagGATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
EST: gi|91048694|gb|EB159112.1|EB159112
EST:     AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG                         GATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
genomic: AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtata ... ctgtgttcagGATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
EST: gi|94475040|gb|EB703998.1|EB703998
EST:     AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG                         GATGTGTTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
genomic: AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtata ... ctgtgttcagGATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
EST: gi|78024373|gb|DV492760.1|DV492760
EST:     AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG                         GATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
genomic: AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtata ... ctgtgttcagGATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
EST: gi|5069938|gb|AI737903.1|AI737903
EST:     AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG                         GATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
genomic: AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtata ... ctgtgttcagGATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
EST: gi|5069940|gb|AI737905.1|AI737905
EST:     AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG                         GATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG
genomic: AAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtata ... ctgtgttcagGATGTGCTTCGGAGGCGCAGGAGCCGCAAAGGCGATGCAGGTTTCTCCCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTGgtacagtatatcaaacttctttctattcgttttgttcctgtatttgacttgatcatattgacatttggactttggctcggtttttttatgagcaattcga

- - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - -  AAGAGA