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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATGCCAGAAGCAGCAGGAGCTGTTGCAGCTGCAGCTGTAGCTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattactgctgtcatttcctctcttatacgactttcagtatttaatcaccagacatcaggagaagccaactttgcttgttggctgttgctatctacc...

Basic information

species Oryza sativa
transcript LOC_Os05g07130.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07130.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G021846_T02 (Zea mays), 5'ss of exon 6
GCCATGCCAGAAGCAGCAGGAGCTGTTGCAGCTGCAGCTGTAGCTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattactgctgtcatttcctctcttatacgactttcagtatttaatcaccagacatcaggagaagccaactttgcttgttggctgttgctatctacc--------
 | |||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||| || || || |||||||||||||||    | ||  |    || | | |||  | ||| |  |||   ||| |    ||  || ||    |   || |||  ||    ||  | || |          
ACAATGCCAGAAGCAGCAGGAGCTGTTGCAGCTGCAGCTGTAGCTGATCGTTTGCATGGGTCAAAGGAGGACCGGAAGCTGGCCATTGTTTTGgtaaatactagttgaaa----ctgtgtgatataattttaaacattct-tcatctcttat--ggtgatttgagtgtttctttgtgatcctt-ttgtcaaaaagataaac

upper sequence: LOC_Os05g07130.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 6
---GCCATGCCAGAAGCAGCAGGAGCTGTTGCAGCTGCAGCTGTAGCTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattactgctgtcatttcctctcttatacgactttcagtatttaatcaccagacatcag-gagaagccaactttgcttgttggctgttgctatctacc-
   || ||||||| ||| || ||||||||||||||||| ||||||||||| |   ||| |||  | || |||||  || |  | || |||||  |||||  || |||   | | |   |   ||  || | |   | | |||||| |    ||   |  || ||  |||  |   | |    |      ||    || 
AATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTGgtat-tttctgtcattactgattgattttgactattcataat-tttaatgatgctactctattgacaattcaatgtgattggaattcaaacattaaaatcct
















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|33381245|gb|CF196588.1|CF196588
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|29616051|gb|CB621063.1|CB621063
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|58695801|gb|CK084488.1|CK084488
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|29615976|gb|CB620988.1|CB620988
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|29616011|gb|CB621023.1|CB621023
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|29615974|gb|CB620986.1|CB620986
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|58688458|gb|CK077145.1|CK077145
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATNGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
EST: gi|29612781|gb|CB617794.1|CB617794
EST:     CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG                         GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG
genomic: CTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattact ... ttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATGCCAGAAGCAGCAGGAGCTGTTGCAGCTGCAGCTGTAGCTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTGgtaaattactgctgtcatttcctctcttatacgactttcagtatttaatcaccagacatcaggagaagccaactttgcttgttggctgttgctatctacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcctctc