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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtccttatttggtgtgttaaatgttacttatatctcttaacaatattatgattgttgagatcctttgtccatctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG

Basic information

species Zea mays
transcript GRMZM2G051842_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051842_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 3'ss of exon 3
gtatgtccttatttggtgtg---tta-aatgttacttatatctcttaacaatattatgattgttgagatcctttgtccatctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
|||   ||||  ||| ||     ||| | |||||||| |  ||||||||| |  || | ||| |  |||| |||   ||| ||||||||||| || || | ||||||||| |||||||||||||||
gta-acccttgcttgatgcagtcttacactgttactttt--ctcttaacagtcgtaggcttgatacgatcatttactcat-taacagGCCAACGAGTTCAAAAAGGAGGACTTCAAAGGCTCCAAG
















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|71446345|gb|DR827395.1|DR827395
EST:     GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
genomic: GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
EST: gi|91057161|gb|EB167579.1|EB167579
EST:     GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
genomic: GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
EST: gi|76293563|gb|DV033131.1|DV033131
EST:     GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
genomic: GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
EST: gi|76286678|gb|DV026246.1|DV026246
EST:     GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCCAG
genomic: GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
EST: gi|71771409|gb|DR969346.1|DR969346
EST:     GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
genomic: GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
EST: gi|78105422|gb|DV523840.1|DV523840
EST:     AGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
genomic: AGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
EST: gi|148987163|gb|EE030992.2|EE030992
EST:     GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
genomic: GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
EST: gi|71447665|gb|DR828715.1|DR828715
EST:     GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
genomic: GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
EST: gi|28569018|gb|CB280893.1|CB280893
EST:     GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTT
genomic: GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTT
EST: gi|149088934|gb|EE178077.2|EE178077
EST:     GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
genomic: GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
EST: gi|148959742|gb|EC905640.2|EC905640
EST:     GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAG                         GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
genomic: GCGGCAACCGCACCATGCGTCCGTGCCTATCTAGCGCAGTCAAGATACAGgtatgtcctt ... catctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttatatctcttaacaatattatgattgttgagatcctttgtccatctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG
          tcttaac  putative branch site (score: 2)
                                    tcctttgtccatct  putative PPT
            ttaacaatattatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtccttatttggtgtgttaaatgttacttatatctcttaacaatattatgattgttgagatcctttgtccatctaacagGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT