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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGGGAGAGGGAAATACAGTGAAGTCTTTGAGGGTATTAATGTTAACAATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagaccatgaatcctattgtatgcagtttgcaacttgttatcccctgaacctactattttagcggtgacaggctactgttttcttttcacacctgtttaaatttcataatttcagtgacaattttcatctcagttttaacatatgcttcttgtgctggtgcag

Basic information

species Zea mays
transcript GRMZM5G845755_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 2
AGTTGGGAGAGGGAAATACAGTGAAGTCTTTGAGGGTATTAATGTTAACAATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagac-------catgaatcctattgtatgcagtttgcaacttgttatcccctgaacctactattttagcggtgacaggctactgttttcttttcacacctgtttaaatttcataatttcagtgacaattttcatctcagttttaacatatgcttcttgtgctggtgcag
|||||||||||| |||||||| || |||||||||||||||||||| ||||| ||||| |||||||| || || || ||||||||||||||||||||||||||||         |||||||||| ||||      |||     |  || |||||||||| | || |||||  ||| ||| | |||||||| | | | ||||||   |   | |||  ||  || |     || | || | |    ||   | |  ||  | ||| |      
AGTTGGGAGAGGAAAATACAGCGAGGTCTTTGAGGGTATTAATGTCAACAACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatgattcatgaatcctgttgtccatccttttt--ttccttttcccctgaacatgctcttttactggtaacatggtactgtttccatcttacacctagctttgtgtca--atggcattagtgtttattattttaaccatagttt-tcttttgtatgcag------
















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|149081763|gb|EE170917.2|EE170917
EST:     ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagaccatg ... gctggtgcagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
EST: gi|148990948|gb|EE032377.2|EE032377
EST:     ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagaccatg ... gctggtgcagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
EST: gi|29946904|gb|CB816382.1|CB816382
EST:     ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagaccatg ... gctggtgcagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
EST: gi|5268357|gb|AI770321.1|AI770321
EST:     ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagaccatg ... gctggtgcagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
EST: gi|149004751|gb|EE039248.2|EE039248
EST:     ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagaccatg ... gctggtgcagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
EST: gi|78115139|gb|DV533527.1|DV533527
EST:     ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagaccatg ... gctggtgcagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
EST: gi|149078770|gb|EE167579.2|EE167579
EST:     TAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACAT
genomic: TAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAA-GAAGgtagaccatg ... gctggtgcagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACAT
EST: gi|31355313|gb|CD439670.1|CD439670
EST:     ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagaccatg ... gctggtgcagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGGGAGAGGGAAATACAGTGAAGTCTTTGAGGGTATTAATGTTAACAATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagaccatgaatcctattgtatgcagtttgcaacttgttatcccctgaacctactattttagcggtgacaggctactgttttcttttcacacctgtttaaatttcataatttcagtgacaattttcatctcagttttaacatatgcttcttgtgctggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG