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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGTCGGAGGTGGTGATGGTGGTGTGCTACGAGAAATAGCCAGACATGCCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagcatcactttatgctttagagtagaattgtcaaattattgttattttaatgattattatgctctcaacctatgcag

Basic information

species Oryza sativa
transcript LOC_Os06g33710.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g33710.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G047867_T01 (Zea mays), 5'ss of exon 6
GGTTGTCGGAGGTGGTGATGGTGGTGTGCTACGAGAAATAGCCAGACATGCCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagcatcacttta----tgctttagagtagaattgtcaaattattgttattttaatgattattatgctctc-aacctatgcag
|||||| |||||||||||||||||||| || || ||||||||||||||||  |||||||| |  || ||||||||||| || || || |||||||||||||||||||  |||||| ||    ||||  | | |  |  | | | | | |   ||| ||  | || | | | ||||| || ||||||||
GGTTGTTGGAGGTGGTGATGGTGGTGTACTGCGCGAAATAGCCAGACATGATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGATgtaagaatgatcactctacctatgctcaaaattcaatgtataatagtgtgaatatattttttatgacttttctctccaaactatgcag
















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|33686636|gb|CF314875.1|CF314875
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|29681267|gb|CB677542.1|CB677542
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|29678039|gb|CB674314.1|CB674314
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|29661773|gb|CB658048.1|CB658048
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|58689103|gb|CK077790.1|CK077790
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|29674257|gb|CB670532.1|CB670532
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|38468529|gb|CF952660.1|CF952660
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|58690531|gb|CK079218.1|CK079218
EST:     CTCAGTGGAGAACATCGANTATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAA-TATCTGT-GGATTCAAAGATCCCCGT
genomic: CTCAGTGGAGAACATCGA-TATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|29660327|gb|CB656602.1|CB656602
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTGTCGGAGGTGGTGATGGTGGTGTGCTACGAGAAATAGCCAGACATGCCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagcatcactttatgctttagagtagaattgtcaaattattgttattttaatgattattatgctctcaacctatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA