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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTATATAAGAAAGAGCGAGATCAGTATGCTGAAGAAGTTAAAGGTGATGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaattgtccactaaatgtgttctcatatgtattggtttattctgcttgttgaaatgctttggaagaagtcagaacaattatgttccttgtatt...

Basic information

species Zea mays
transcript GRMZM2G484880_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G484880_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g34300.2 (Oryza sativa), 5'ss of exon 9
CTTTTATATAAGAAAGAGCGAGATCAGTATGCTGAAGAAGTTAAAGGTGATGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaattgtccactaaatgtgttctc-atatgtattggtttattctgcttgttgaaatgctttggaagaagtcagaacaattatgttccttgtatt
||||| ||||||||||||||| | |||||  ||||||| |||||||| ||||| || || |||||| |||||||||||||||||||| ||||||||||||||| || || || |  | || ||| | | || |    |    | |||||| |     | |          | |||   ||    ||| | |       | |
CTTTTGTATAAGAAAGAGCGACAGCAGTACTCTGAAGAGGTTAAAGGCGATGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcagttcttgattacatgagatatccaccaatgaatgattattcagtaaagtaaggaaacaattaggaa-caaggtttattgtctgttcaaaagt

upper sequence: GRMZM2G484880_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g01130.1 (Oryza sativa), 5'ss of exon 9
CTTTTATATAAGAAAGAGCGAGATCAGTATGCTGAAGAAGTTAAAGGTGATGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaattgtccactaaatgtgttctcatatgtattggtttattctgcttgttgaaatgctttggaagaagtcagaacaat-tatgttccttgtatt----
||||||||||||||||| | | | |||||  ||||||| |||||||||||||| || || |||| | |||||||||| ||||||||| ||||||||||||||| || || || || | || ||| | | ||  |   ||   |  ||| |  |   | || |     | || || |  ||||||  | | ||   |||       
CTTTTATATAAGAAAGAACAACAGCAGTACACTGAAGAGGTTAAAGGTGATGTTTCGCCCTCAATTATATATGGAGCCGAGCATCTACTGCGCCTTTTTGgtatgtgcagttctcgattatatgagatatc-caccaatgaataaattat--tcagtaaagtaag--gaaacaattaggaacaaggtttattgtctgttcaaaat

upper sequence: GRMZM2G484880_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv07s0129g01020.t01 (Vitis vinifera), 5'ss of exon 9
CTTTTATATAAGAAAGAGCGAGATCAGTATGCTGAAGAAGTTAAAGG---TGATGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaattgtc--cactaaatgtgttctcatatgtattg-gtttattctgcttgttgaaatgctttggaagaagtcagaacaattatgttccttgtatt
   |||||||| ||||||||  | || | |   |||| | || |      |||| |||| ||||||||||||||||| || ||||||||  ||||||| ||||||| |      |       || || | ||| | || || || | ||||  | |  ||| | | |   | |  |  | |      | || |  |   |  |   
---TTATATAAAAAAGAGCGTCAACAATTTCAAGAAGCAATTTACCACCCTGATCTCTCTCCATCAACTGTATATGGCGCAGAGCATCTGCTGCGCCTCTTTGgtatgcttctctagaagtgctgaa-gcgttttaat-tgcatggagttttgtttatttggtaacagtgtcttaagaaggcttattccatgaaatatttaatga-

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|5762213|gb|AI967261.1|AI967261
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|60343282|gb|DN210255.1|DN210255
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|211181083|gb|FL441231.1|FL441231
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|78544095|gb|DV621593.1|DV621593
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|31997933|gb|CD661838.1|CD661838
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|211056265|gb|FL131318.1|FL131318
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTKTG                         TGAAATTGCCAGAGCTACTTGC
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGC
EST: gi|37386752|gb|CF630565.1|CF630565
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|211165206|gb|FL438738.1|FL438738
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|20208496|gb|BQ134585.1|BQ134585
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCCTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|33103032|gb|CF062992.1|CF062992
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TGAAATTGCCAGAGCTACTTGCTTCTGTTAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|6020484|gb|AW065412.1|AW065412
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|32866884|gb|CF006566.1|CF006566
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TGAAATTGCCAGAGCTACTTGCTTCTGTTAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|211399030|gb|FL440153.1|FL440153
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TGAAATTGCCAGAGCTACTTGCTTCTGTTAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|22546503|gb|BU098814.1|BU098814
EST:     TGTCTTACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|22546502|gb|BU098813.1|BU098813
EST:     TGTCTTACCCTCAACTGTATATGGAGCTGAGCATCTATTGCCCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|9952124|gb|BE638722.1|BE638722
EST:     GTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: GTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|71759434|gb|DR957371.1|DR957371
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|32937879|gb|CF042698.1|CF042698
EST:     GTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TGAAATTGCCAGAGCTACTTGCTTCTGTTAATATGGAGGAAGATGCGTTGA
genomic: GTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|93284202|gb|EB676466.1|EB676466
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|8666010|gb|BE186826.1|BE186826
EST:     CTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: CTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|211058553|gb|FK994418.1|FK994418
EST:     CTATTGCGCCTTTTTG                         TGAAATTGCCAGAGCTACTTGCTTCTGTTAATATGGAGGAAGATSCGTTGA
genomic: CTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
EST: gi|5917408|gb|AW054199.1|AW054199
EST:     TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTG                         TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA
genomic: TGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaa ... aagtttgcagTAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTTATATAAGAAAGAGCGAGATCAGTATGCTGAAGAAGTTAAAGGTGATGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaattgtccactaaatgtgttctcatatgtattggtttattctgcttgttgaaatgctttggaagaagtcagaacaattatgttccttgtatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagaacaa