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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgatatccttgctctatttgccacatcttaacttttttgttgcaccattaagacacgtatgagaccagtcatcgtgtactcctgaagGGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTTCTGGCCTCATCTGATTCAGATGGCACAGTTATCGTATGGAAGCGATCGA

Basic information

species Zea mays
transcript GRMZM2G093239_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093239_T04 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g56860.1 (Oryza sativa), 3'ss of exon 11
gtatgtgatatccttgctctatttgccacatcttaacttttttgttgcaccattaagacacgtatgagaccagtcatcgtgtactcctgaagGGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTTCTGGCCTCATCTGATTCAGATGGCACAGTTATCGTATGGAAGCGATCGA
||||||    | |||  |||||||     |||||||  |||  ||| ||     |||  ||  |||| || | |     |  | || ||||||||||||||||||||||||| ||||| ||||||| ||| ||||| ||||| || |||||||||||||||||||| |||||||| |||||||||||  |  
gtatgttcagtgcttcttctatttttggaatcttaaactttg-gttccatggcaaaggtaccgatgaaactatt-----ttcattcgtgaagGGACATGGTTCTCCAGTAATTGGAGTGGCCTGGAGTCATGGGGAAAATTTGCTTGCCTCATCTGATTCAGATGGTACAGTTATTGTATGGAAGCGGGCAT
















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|113700998|gb|EE678502.1|EE678502
EST:     ACTTCTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAG                         GGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
genomic: ACTTCTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAGgtatgtgata ... actcctgaagGGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
EST: gi|78108751|gb|DV527168.1|DV527168
EST:     ACTTCTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAG                         GGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
genomic: ACTTCTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAGgtatgtgata ... actcctgaagGGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
EST: gi|71431087|gb|DR812137.1|DR812137
EST:     ACTTTTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAG                         GGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
genomic: ACTTCTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAGgtatgtgata ... actcctgaagGGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
EST: gi|32870682|gb|CF010364.1|CF010364
EST:     ACTTCTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAG                         GGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
genomic: ACTTCTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAGgtatgtgata ... actcctgaagGGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
EST: gi|101384844|gb|EB814468.1|EB814468
EST:     ACTTTTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAG                         GGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
genomic: ACTTCTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAGgtatgtgata ... actcctgaagGGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
EST: gi|76908768|gb|DV163090.1|DV163090
EST:     ACTTTTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAG                         GGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT
genomic: ACTTCTATGATTTGGCACGCCCAAAGAATTCGTGTGTGAACAAACTACAGgtatgtgata ... actcctgaagGGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgttgcaccattaagacacgtatgagaccagtcatcgtgtactcctgaagGGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTTCTGGCCTCATCTGATTCAGATGGCACAGTTATCGTATGGAAGCGATCGA
                                            tactcct  CT-rich tract
              attaaga  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgatatccttgctctatttgccacatcttaacttttttgttgcaccattaagacacgtatgagaccagtcatcgtgtactcctgaagGGACATGGTTCTCCAGTAATCGGAGTTGCCTGGAATCACGGGGAGAATTTTCTGGCCTCATCTGATTCAGATGGCACAGTTATCGTATGGAAGCGATCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG