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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccggtgatcacattgatttgttgtaatatttctattatactttgtaatacatatatttatcattagtaacatatctgatattttaataattcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCG

Basic information

species Oryza sativa
transcript LOC_Os09g07830.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 6
ccggtgatca-cattgatttgttgtaatatttctat-tatactttgtaatacatatatttatcattagtaacatatctgatattttaataattcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCG
|   | ||   || | || ||||| ||| | | | | | ||  ||| |||| ||||||||   |||  |   |||| | |  ||||| | ||||||  ||||||||| | |||||| |||||||| ||||||||||||||||||||  |||||||||||||||||||||||||| |||||
cttttaattttcacttatatgttgcaatttatttttgtctatattgcaataaatatatttccaatttctggtatatttaa--ttttacttattcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 6
--ccggtgatcacattgatttgttgtaatatttctat-tatactttgtaataca-tatatttatcattagtaacatatctgatattttaataattcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCG
      |     |    || || ||  || | | | | | ||  ||| | | || ||| |||  ||||  |    |||     |||||| |  ||  |  ||||||||| | |||||| ||||||||  |||||||||||||||||||  ||||||||||||||||||||||||||||||||
tgagaatatcttcccatatatgatgctatgtatttttgtttatattgcactgcaatatgtttg-catttctggtgtattg---attttacttgtttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTGTTCCG

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 4
ccggtgatcacattgatt--tgttgtaatat-ttctattatactttgtaatacatatatttatcattagtaacatatctgatattttaataattcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCG
  ||  ||    ||| ||  |||| |||| | || |  | ||  ||| |||| ||||||||   |||  |   |||| |||  ||||| | ||||||  ||||||||| | | |||| | |||||| || ||||||||||| |||||  ||||||||||||||||||||||||||||||| 
-aggctatattgttgtttgttgttttaatgtattttcatctatattgcaataaatatatttccaatttctggtatatttga--ttttacttattcttgcatagGATGCATTTTCTATCCGAAGCAACGAACGTGGAATTGCAGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTGTTCCA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G085474_T02 (Zea mays), 3'ss of exon 6
--ccggtgatcacattgatttgttgtaatatttctat-tatactttgtaataca-tatatttatcattagtaacatatctgatattttaataattcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCG
      |     |    || || ||  || | | | | | ||  ||| | | || ||| |||  ||||  |    |||     |||||| |  ||  |  ||||||||| | |||||| ||||||||  |||||||||||||||||||  ||||||||||                      
tgagaatatcttcccatatatgatgctatgtatttttgtttatattgcactgcaatatgtttg-catttctggtgtattg---attttacttgtttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGTGGTGC----------------------

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|58685561|gb|CK074248.1|CK074248
EST:     ATTGTGCTGAGCTTTGTGCTGACAATCATGCTCTGACAAGGGAAGACCAG                         GATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGT
genomic: ATTGTGCTGAGCTTTGTGCTGACAATCATGCTCTGACAAGGGAAGACCAGgtattttttt ... tcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGT
EST: gi|29640957|gb|CB645964.1|CB645964
EST:     ATTGTGCTGAGCTTTGTGCTGACAATCATGCTCTGACAAGGGAAGACCAG                         GATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGT
genomic: ATTGTGCTGAGCTTTGTGCTGACAATCATGCTCTGACAAGGGAAGACCAGgtattttttt ... tcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGT
EST: gi|33678061|gb|CF306300.1|CF306300
EST:     ATTGTGCTGAGCTTTGTGCTGACAATCATGCTCTGACAAGGGAAGACCAG                         GATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGT
genomic: ATTGTGCTGAGCTTTGTGCTGACAATCATGCTCTGACAAGGGAAGACCAGgtattttttt ... tcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacatatatttatcattagtaacatatctgatattttaataattcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCG
                                            ttcttctat  CT-rich tract
     atatatttatcattag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccggtgatcacattgatttgttgtaatatttctattatactttgtaatacatatatttatcattagtaacatatctgatattttaataattcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT