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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatatttgcatgccaaactgtcttattatctctagctcttgcccatgaccagtaatcatcagttgtacgtgtggtcagtatgattatttccatat...

Basic information

species Oryza sativa
transcript LOC_Os02g17320.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G169462_T01 (Zea mays), 5'ss of exon 5
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatatttgcatgccaaactgtcttattatctctagctcttgcccatgaccagtaatcatcagttgtacgtgtggtcagtatgattattt-ccatat-
|| |||||||| ||||| |||||||||||||||||||| ||||| ||||||||||| || |||||||||||||||||||||| || ||||| ||||||| |||||||||| | | | || | ||| | |||||||| | | | || |||| || ||||| | ||||
GTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATTTTCGTTGATACAGgtaccaatatttgcttataagttgatgttttcttctgtctctcttgcctgtcgatatt--ccagaagttcccaatgcacaagcattgattcccgactatatt

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 6
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatatttgcatgccaaactgtcttattatctctag---ctcttgcccatgaccagtaatcatcagttgtacgtgtggtcagtatgattatttccatat
|| |||||||||||||| |||||||||||||||||||| ||||| ||||||||||| || ||||||||||||||||||||||||| ||||| ||||||| ||||||||| | | | | || ||| | | |||||| | | | || |||| || || || | | |||
GTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAGgtacaaatatttgcttataagttgatgatgttttcttctgtctcccttgcctgttgatatt--ccagaagttcccaatgca-caagcattgattcctgactat

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA18G08180.1 (Glycine max), 5'ss of exon 6
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgta--tcaatatttgcatgccaaactgtcttattatctctagctcttgcccatgaccagtaatcatcagttgtacgtgtggtcagtatgattatttccatat
| || ||||||||||| || ||||| ||||| || || |||||||||||| ||||||| ||||| |||||||| |||||||| ||||||||||||||| | | |||| || ||| || | | || | ||| | || | | | | | || | | || || |
-TGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGGtcctttattattgttattccat-ctttaactcagaatttatttattgtaagtttgttgttgtatttgttaatttataagggaaatggtccatcttttatct

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G45270.1 (Glycine max), 5'ss of exon 6
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatatttgcatgccaaactgtcttattatctctagctcttgcccatgaccagtaatcatcagttgtacgtgt-ggtcagtatg--attatttccatat--
|| || ||||||||||| || ||||||||||| || || ||||||||||| ||||||| ||||| |||||||| |||||||| ||||||||||||||| | |||| | | |||| || || | | | | ||| ||||||||| ||| || ||| | || | ||| |
GTGAACCCTTCAGATGTTATAATTTTGGAAGGCATCCTTGTTTTCCATGACCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGgt-cctttattattgttttt--ccatctt--taattcagaatttatttttttattgtaaattttcagttgtatttgttagtttgtaagggatatggttcatcttt

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G47270.1 (Glycine max), 5'ss of exon 6
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatc--aatatttgcatgccaaactgtcttattatctctagctcttgcccatgaccagtaatcatcagttg-tacgtgtggtcagtatgattatttccatat
|| || || | ||||| |||||||||||||| || || ||||| |||||| |||| || || | |||||||| |||||||| ||||||||||||||| | | ||||| | |||| | ||| ||| || || | || ||| || || || ||| | | | | |||
GTAAACCCAGCGGATGTTATTATTTTGGAAGGTATCCTTGTTTTTCATGATCCACGAGTGCGAGCATTGATGAATATGAAGATATTTGTTGACACAGgtcccttattattttagttccaatataactt-ctataacttactgtattatatttttctgtggcatttcttactatgtatggatc-tgttgtcaaactcatt-

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 6
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatatttgcatgccaaactgtcttattatctctagctcttgcccatgaccagtaatcatcagttgtacgtgtggtcagtatgattatttccatat--------------------------------------------------------------------------------
|| |||||| |||||||||| ||| | ||||| || || | ||||||||| |||| ||||| | ||||||||||||||||| |||||| |||||||| | | |||| | | | | | ||||| | |||||| ||| | ||| | || ||| | || | ||| | |
GTAAATCCTACAGATGTAATAATTCTTGAAGGGATACTTTTGTTCCATGATCCACGCGTCCGAAAGTTGATGAACATGAAGATTTTTGTTTGCACAGgta--atttgttgcct-cttcccgttataattattgtaaactcttgttt-cgactacattccatttcccttttgtagattcact-tggctttttttttctacaaaatttcacatgatggaacaacttcttatgctttaagattttgctgtttcacattgcttattttgttttctgcgtag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 6
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatatttgcatgccaaactgtcttattatctctagctcttgcccatgacc-agtaatcatcagttgtacgtgtggtcagtatgattatttccatat
||||| ||||||||||| || ||||||||||| || || |||| |||||| ||||||||||| ||||||||||||||||| |||||||| |||||| || | | | | ||| | |||| | || | | | || | || | | || | || | | || |
GTCAACCCTTCAGATGTGATAATTTTGGAAGGCATACTCATTTTTCATGATCTTCGTGTCCGGGAATTGATGAACATGAAGATATTTGTTGATACAGgttctttctttctgcctttactgcagaatgtcaattcttgtacttggtcttgtcttatttattaatagcttt-tgtccaggcatgaactgtgcttttagtc

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S370_24V6.1 (Physcomitrella patens), 5'ss of exon 4
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgt-------atcaatatttgcatgccaaactgtcttattatctctagctct---tgcccatgaccagtaatcatcagttgtacgtgtggt---cagtatgattatttccatat--------------------------------------------------------
|| ||| | || ||||| ||||| ||||| || || || | || || ||| || || || || || ||||| |||||||||||||||||||||||| | ||| | | | | | | || || || | || | ||||| | || |||| | | | || | | | | ||
GTAAATGCGTCTGATGTCATTATCTTGGAGGGGATACTAATCTTTCACGATGTTCGAGTTCGTGAATTCATGAATATGAAGATCTTTGTTGACACAGgtcagcattgtaaatcatcacctaacgcaataactcgtttctgtaaggccgctgtgattttctgcagtagttattagttcttggcctaccatgcaacccgctgaaaccggtagtcattgaggccagtatcgcatctccatagggactcatgttgaactgtgcagtgcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S488_8V6.1 (Physcomitrella patens), 5'ss of exon 5
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatatttgcatgccaaactgtcttattatctctagctcttgcccatgaccagtaatcatc----agttgtacgtgtggtcagtatgattatttccatat---------------------------------------------
|| ||| | || || || | || ||||| || ||| |||| ||||||||| | ||||| ||||| | ||||||||||| ||||||||||| |||||| | | | |||| | | | || | ||| ||| | || | || | |||| | | ||| | || ||| | || |
GTGAATGCATCTGACGTGGTCATCTTGGAGGGCATTTTGGTCTTCCATGATGCTCGTGTTCGGGAGCTTATGAACATGAAAATCTTTGTTGATACAGgt-tagccctctctatgc-atttcgcttgccgccctttggcttttgttatcaattagcacccaactcgtgaatgtagatatattcattctggatatgttcaaaggtcagacctccttcatagggactcatatttttctttgcaatacag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S83_234V6.2 (Physcomitrella patens), 5'ss of exon 6
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatatttgca--tgccaaactgtcttat-tatctctagctcttgccc--atgacca------gtaatcatcagttgtacgtgtggtcagtatgattatttccatat--------------------------------------------------------------------------------
|||||| | || |||||||||||| |||| ||||| || | || |||||| | ||||| ||||| | ||||| ||||||||||||||||| |||||| || ||| | | | || |||| || |||| | ||| | ||| || | | | | || | | ||| ||| | | || |
GTCAATGCATCTGATGTAATTATTGTGGAGGGAATATTGATCTTTCATGATGCTCGTGTTCGGGAGTACATGAATATGAAGATCTTTGTTGATACAGgt--cagcattgagaatcattacccagttttatatagctcttggtctcattctaatgtgtgtttgaggtcacctttgttagtttcttgaatgagttagatattctgcacctactgcacaacccgttatgagttggctcttgaagccagagacgtgtcggctcggacactcatcttgaacagtgcagtgcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ31180 (Selaginella moellendorffii), 5'ss of exon 5
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatatttgcatgccaaactgtcttattatctctagctcttgcccatgaccagtaatcatcagttgtacgtgtggtcagtatgattatttccatat
|| ||| | ||||||| || || |||||||||| |||||||||||||| || || || ||| |||||||||||||||| ||||| ||||||||| | || || | ||| | | ||| | ||||| | || |
GTGAATGCAGCAGATGTTATAATCCTGGAAGGAATCCTGGTTTTCCATGACAGTCGCGTTCGTGATCTGATGAACATGAAGATTTTTGTCGACACAGgtttgccgcttctttggctatcctggcattttagaagt-gctctc-cacaccgcag--------------------------------------------

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|33675270|gb|CF303509.1|CF303509
EST:     TGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAG                         ATGCTGATGTGCGATTAACAAGGAGGATTCTACGTGACACCATTGAGAAGG
genomic: TGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatat ... gaattttcagATGCTGATGTGCGATTAACAAGGAGGATTCGACGTGACACCATTGAGAAGG
EST: gi|29643325|gb|CB648332.1|CB648332
EST:     TGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAG                         ATGCTGATGTGCGATTAACAAGGAGGATTCGACGTGACACCATTGAGAAGG
genomic: TGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatat ... gaattttcagATGCTGATGTGCGATTAACAAGGAGGATTCGACGTGACACCATTGAGAAGG
EST: gi|44678675|gb|CR292109.1|CR292109
EST:     TGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAG                         ATGCTGATGTGCGATTAACAAGGAGGATTCGACGTGACACCATTGAGAAGG
genomic: TGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatat ... gaattttcagATGCTGATGTGCGATTAACAAGGAGGATTCGACGTGACACCATTGAGAAGG
EST: gi|33794950|gb|CF323355.1|CF323355
EST:     TGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAG                         ATGCTGATGTGCGATTAACAAGGAGGATTCGACGTGACACCATTGAGAAGG
genomic: TGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatat ... gaattttcagATGCTGATGTGCGATTAACAAGGAGGATTCGACGTGACACCATTGAGAAGG
EST: gi|58591679|gb|CF989987.1|CF989987
EST:     TGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAG                         ATGCTGATGTGCGATTAACAAGGAGGATTCGACGTGACACCATTGAGAAGG
genomic: TGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatat ... gaattttcagATGCTGATGTGCGATTAACAAGGAGGATTCGACGTGACACCATTGAGAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAGgtatcaatatttgcatgccaaactgtcttattatctctagctcttgcccatgaccagtaatcatcagttgtacgtgtggtcagtatgattatttccatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA