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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaatgctggtctgctgttcacacttttgcatcacaaggagttatgtgctatgttgtggaaagcgaaagctttaccctcttttttttacatacttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGTACACTTTTGCATCCATACCAGATTATTAGCCTTTCAGTTTGCGCTGCTG

Basic information

species Zea mays
transcript GRMZM2G042881_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042881_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g03500.2 (Oryza sativa), 3'ss of exon 2
aacaatgctggtctgctgttcacacttttg-catcacaaggagttatgtgctatgttgtggaaagcgaaagctttaccctcttttttttacata--cttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGTACACTTTTGCATCCATACCAGATTATTAGCCTTTCAGTTTGCGCTGCTG
   ||     |||   ||||   | | | |  |  | |  ||  | | | ||||  | |  |    |  ||    |   | || || | ||||    ||| |||||| || ||||||||||||||||||||||| | | | |||||||||||||| || |||||||| || ||||||||||| |||| || | |   |   ||
---aaattatgtcctttgttattattgtagatagtagacagacatctctactattgtatccatttagcgagaaggattatattgttctgacattgttttgtagGTTTTTATGAGACTCGAGTTGCTTACTATTCCTCGAGAGGAGCACCAGGGTATACCTTTGCATCTATTCCAGATTATTAACCTTCCATTGTTTTCATTTG

upper sequence: GRMZM2G042881_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g03760.1 (Oryza sativa), 3'ss of exon 2
aacaatgctg-gtctgctgttcacacttttgcatcacaaggagttatgtgctatgttgtggaaagcgaaagctttaccctcttttttttacata--cttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGTACACTTTTGCATCCATACCAGATTATTAGCCTTTCAGTTTGCGCTGCTG--
   ||   |  |||   |||| |   || |  ||   |   || | |   ||||  | |  |    |  || |  |   | || || | ||||    ||| |||||| || ||||||||||||||||||||||| | | | || |||||||| ||||| |||||||| || ||||||||||| |||| ||  |||     |    
tgtaaaattatgtcctttgtt-attgttgtagatagtagacagctcta--ctattgtatccatttagcgagatggattatattgttctgacattgttttgtagGTTTTTATGAGACTCGAGTTGCTTACTATTCCTCGAGAGGGGCACCAGGATACACCTTTGCATCTATTCCAGATTATTAACCTTCCA--TTGTCTCACCAAG

upper sequence: GRMZM2G042881_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g03500.1 (Oryza sativa), 3'ss of exon 2
aacaatgctggtctgctgttcacacttttg-catcacaaggagttatgtgctatgttgtggaaagcgaaagctttaccctcttttttttacat--acttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGTACACTTTTGCATCCATACCAGATTATTAGCCTTTCAGTTTGCGCTGCTG
   ||     |||   ||||   | | | |  |  | |  ||  | | | ||||  | |  |    |  ||    |   | || || | ||||    ||| |||||| || ||||||||||||||||||||||| | | | |||||||||||                                                   
---aaattatgtcctttgttattattgtagatagtagacagacatctctactattgtatccatttagcgagaaggattatattgttctgacattgttttgtagGTTTTTATGAGACTCGAGTTGCTTACTATTCCTCGAGAGGAGCACCAGG---------------------------------------------------

upper sequence: GRMZM2G042881_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT3G29170.1 (Arabidopsis thaliana), 3'ss of exon 2
-aacaatgctggtctgctgttcacacttttgcatcacaaggagttatgtgctatgttgtggaaagcgaaagctttaccctcttttttttacatacttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGTACACTTTTGCATCCATACCAGATTATTAGCCTTT--CAGTTTGCGCTGCTG
    |||  | || |  | ||      | |  | |       | | || |  | |  ||| |     |  || ||  |   |||   |    |   | |||||||||||||||| ||| |||||||||| |||||| | |||||   |||||||  ||||||| |||| ||   ||| |   ||     |  | | |  |   
ttgaaatcatcgtttctttttttgttctctttacctatgtatgctgtgagtaaagcagtg-attttcatggccttgacacatttcactattgtggctacagGTTTCTACGAGACCCGAATTGCTTACTACTCATGGAGAGGAGCTGAAGGGTACCGTTTTGCAGCCATTCCCTCTTACTGAACTCAAGTAACTGGAGAAGT--

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|93011661|gb|EB637181.1|EB637181
EST:     CATTTCATGCCTAGGCAACACCTAATCATATAGGGCGGATGCATCCCGAG                         GTTTTTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGT
genomic: CATTTCATGCCTAGGCAACACCTAATCATATAGGGCGGATGCATCCCGAGgttgtggcga ... atacttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGT
EST: gi|71330250|gb|DR801871.1|DR801871
EST:     CATTTCATGCCTAGGCAACACCTAATCATATAGGGCGGATGCATCCCGAG                         GTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGT
genomic: CATTTCATGCCTAGGCAACACCTAATCATATAGGGCGGATGCATCCCGAGgttgtggcga ... atacttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGT
EST: gi|71322065|gb|DR797721.1|DR797721
EST:     CATTTCATGCCTAGGCAACACCTAATCATATAGGGCGGATGCATCCCGAG                         GTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGT
genomic: CATTTCATGCCTAGGCAACACCTAATCATATAGGGCGGATGCATCCCGAGgttgtggcga ... atacttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGT
EST: gi|76291966|gb|DV031534.1|DV031534
EST:     CATTTCATGCCTAGGCAACACCTAATCATATAGGGCGGGTGCATCCCGAG                         GTTTCTTCGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGT
genomic: CATTTCATGCCTAGGCAACACCTAATCATATAGGGCGGATGCATCCCGAGgttgtggcga ... atacttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGT
EST: gi|71299618|gb|DR785819.1|DR785819
EST:     CATTTCATGCCTAGGCAACACCTAATCATATAGGGCGGATGCATCCCGAG                         GTTTTTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGT
genomic: CATTTCATGCCTAGGCAACACCTAATCATATAGGGCGGATGCATCCCGAGgttgtggcga ... atacttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgctatgttgtggaaagcgaaagctttaccctcttttttttacatacttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGTACACTTTTGCATCCATACCAGATTATTAGCCTTTCAGTTTGCGCTGCTG
                         ctttaccctctttttt  CT-rich tract
                                   ttttttttacatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaatgctggtctgctgttcacacttttgcatcacaaggagttatgtgctatgttgtggaaagcgaaagctttaccctcttttttttacatacttgcagGTTTCTACGAGACTCGAGTTGCTTACTATTCATGGCGGGGAGCACCAGGGTACACTTTTGCATCCATACCAGATTATTAGCCTTTCAGTTTGCGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT