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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttggaatccctttgatattggcattcatcttttctttgttctgtaattcttgcctttttcttgtaaatagatttagactttaccttttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG

Basic information

species Zea mays
transcript GRMZM5G820727_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G820727_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g34750.1 (Oryza sativa), 3'ss of exon 2
ttttttggaat-ccctttgatattggcattcatcttttctttgttctgtaattcttgcctttttcttgtaaatagatttagactttaccttttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG
| |  ||  |   | |||   |||     ||   || |  |||||          |    ||||| |||||  ||||||||| |   |  ||   |||||||||| |||||||| || || || || |||||||| || |||||  | |||||||||||||| |||||||||
tatgatgatacatcatttatcattccttctctagttatggttgtttcagtcactatcttgttttcctgtaataagatttagattgc-cacttcgcatgcagGAAGCCAGTGCAATTCGGCTACACAAACATTTGACGGAGTTGACCTGATGGGTGAAAGGTTGGCAAATGAG

upper sequence: GRMZM5G820727_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G25770.1 (Arabidopsis thaliana), 3'ss of exon 2
ttttttggaatccctttgatattggcattcatcttttctttgttctgtaattcttgcctttttcttgtaaatagatttagactttaccttttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG
   |  |   | | |    ||| |  |||    ||||  ||  ||||||||| |    ||| | |  |    |   | | | |  |      | | ||||| ||  || | ||   ||| ||   |||||||||||||||||||  ||||||||||||| |||| ||||||
--gtgcgtgtttcttgacctatagatattgtggttttgattactctgtaattttatgatttgtttgattttgatgatgaaattgga------tgaagcagGTAGCGAGAGTAATAGTGCAACGTTGACATTTGATGGTGTTGATAAAATGGGTGAAAGGCTAGCTAATGAG
















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|71772904|gb|DR970827.1|DR970827
EST:     CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC                         GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
genomic: CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACCgtgagttacc ... ttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
EST: gi|78113514|gb|DV531905.1|DV531905
EST:     CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC                         GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
genomic: CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACCgtgagttacc ... ttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
EST: gi|148942263|gb|EC887279.2|EC887279
EST:     CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC                         GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGT
genomic: CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACCgtgagttacc ... ttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGT
EST: gi|76020655|gb|DT947825.1|DT947825
EST:     CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC                         GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
genomic: CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACCgtgagttacc ... ttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
EST: gi|78090975|gb|DV519349.1|DV519349
EST:     CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC                         GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
genomic: CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACCgtgagttacc ... ttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
EST: gi|78082075|gb|DV510487.1|DV510487
EST:     CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC                         GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
genomic: CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACCgtgagttacc ... ttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
EST: gi|78106692|gb|DV525110.1|DV525110
EST:     CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC                         GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG
genomic: CGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACCgtgagttacc ... ttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaattcttgcctttttcttgtaaatagatttagactttaccttttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG
                                    ctttaccttttttat  CT-rich tract
             tttttcttgtaaatag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttggaatccctttgatattggcattcatcttttctttgttctgtaattcttgcctttttcttgtaaatagatttagactttaccttttttatgcagGAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG

- - - - - - - - - - - - gcattca
- - - - - - - - - - - - - - - - - - - - tgttctg