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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttctgctccttaagtatcttcacccgtcatacctgttatcatattctctaggttgctggcagtatgagtttgctgtatttattcgtgctcatccaatgccag

Basic information

species Oryza sativa
transcript LOC_Os04g40740.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40740.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 15
CCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttctgctccttaagtatct-tcacccgtcatacctgttatcatattctctaggttgctggcagtatgagtttgctgtatttattcgtgctcatccaatgccag
|| ||||| ||||| | ||||||||||||||| ||  ||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||||   | ||  | | ||  |||   ||||     | ||  ||||  ||        |   |  | |    || || || || || ||  || |||| | |||
CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttccatttctcgaatttccatcattggtca-----gctagtatatcatcc------ttaataaaacg----tgttgcatgtaatcctgtacacccaacggcag

upper sequence: LOC_Os04g40740.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 5'ss of exon 18
CCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttctgctccttaagtatcttcacccgtcatacctgttatcatattctctaggttgctggcagtatgagtttgctgtatttattcgtgctcatccaatgccag
|| |||||  |  | || || ||||| ||| | ||  || |||||||||| ||||| ||| ||||||||||||||||||||||||||||  |||  |     ||||   |        | |||   || | || ||  |||| | |   || |    | | ||||||  |   ||   |  | |    | |  | 
CCTGGAGAAACCTTGAAGGACTTCTATAAGCGTACCAATTTGTACTGGCAAATGGCAGCACATGAGCACACTCAACACACTGGAAAGgtctgttcataagttttaatattagctggtagacat-tttgctctcttag-ctcttgttcattgtct---tcaatttgcttgaccaatcaat--tgaggtgaaggta-

upper sequence: LOC_Os04g40740.1 (Oryza sativa), 5'ss of exon 18
lower sequence: EFJ09772 (Selaginella moellendorffii), 5'ss of exon 16
CCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttctgctccttaagtatcttcacccgtcatacctgttatcatattctctaggttgctggcagtatgagtttgctgtatttattcgtgctcatccaatgccag
|| || ||  | || | |||||| | |    | |||   ||||| ||||| |||||||| || || ||||| ||||||||||||||||| |     ||   |     |   ||| | |||  | | || | |     ||| |  |                                                  
CCTGGGGAAACGCTGAGAGATTTTTTCTCCCGGACGATCATGTATTGGCAAATGGCTGCTTACGACCACACCCAACACACTGGAAAGgtga-----tgacgcaggttttctttcgctcgttcttcatgctctttgcatctatcag--------------------------------------------------

upper sequence: LOC_Os04g40740.1 (Oryza sativa), 5'ss of exon 18
lower sequence: EFJ11619 (Selaginella moellendorffii), 5'ss of exon 16
CCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgtta-gtttctgctccttaagtatcttcacccgtcatacctgttatc-atattctctaggttgctggcagtatgagtttgctgtatttattcgtgctcatccaatgccag
|| || ||  | || | |||||| | |    | |||   ||||| ||||| |||||||| || || ||||| ||||||||||||||||| | |   | | |  ||     | ||| | |||  | | || | |  | ||     ||                                                   
CCTGGGGAAACGCTGAGAGATTTTTTCTCCCGGACGATCATGTATTGGCAAATGGCTGCTTACGACCACACCCAACACACTGGAAAGgtgatgacgcaggttttt-----ttttcgctcgttcttcatgctctttacatctatcag---------------------------------------------------

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|3760761|gb|C98015.1|C98015
EST:     ATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG                         GA-NTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
genomic: ATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttct ... ccaatgccagGAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
EST: gi|86534966|gb|CI175172.1|CI175172
EST:     ATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG                         GAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
genomic: ATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttct ... ccaatgccagGAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
EST: gi|29631150|gb|CB636159.1|CB636159
EST:     CATATGAGCGCACTCAACACACTGGAAAG                         GAGCTCCGCAAAGATGGTTTTGATCTGGCCGAAACTCGATATAAGGAATTG
genomic: CATATGAGCACACTCAACACACTGGAAAGgttagtttct ... ccaatgccagGAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
EST: gi|88266525|gb|CI377427.1|CI377427
EST:     CTGGCAGATGGGCTGCATATGAGCACACTCAACACACTGGAAAG                         GAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
genomic: CTGGCAGAT-GGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttct ... ccaatgccagGAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
EST: gi|89175699|gb|CI042720.1|CI042720
EST:     ATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG                         GAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
genomic: ATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttct ... ccaatgccagGAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
EST: gi|88264898|gb|CI367549.1|CI367549
EST:     ATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG                         GAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
genomic: ATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttct ... ccaatgccagGAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
EST: gi|286456|gb|D15264.1|D15264
EST:     ATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG                         GAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
genomic: ATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttct ... ccaatgccagGAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
EST: gi|88849715|gb|CI089821.1|CI089821
EST:     CACACTCAACACACTGGAAAG                         GAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG
genomic: CACACTCAACACACTGGAAAGgttagtttct ... ccaatgccagGAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttctgctccttaagtatcttcacccgtcatacctgttatcatattctctaggttgctggcagtatgagtttgctgtatttattcgtgctcatccaatgccag

- - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - CAGATG