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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaccctggtcttgagttttttgtctggattaaataagcattgtgttcataccagtgacccagtttgatcttggcttcacttctattatcttccagCTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAATGTGATTCCATTACGACTAGGCTATGTTGGTGTGGTAAACCGCAGTCAAC

Basic information

species Oryza sativa
transcript LOC_Os01g69130.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 3
---gtttgaccctggtcttgagttttttgtctggattaaat---aagcattgtgttcatacca-gtgacccagtttgatcttggcttcacttctattatcttccagCTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAATGTGATTCCATTACGACTAGGCTATGTTGGTGTGGTAAACCGCAGTCAAC
    |||    ||   ||| |  ||  | ||    ||| ||      |||  | |   | |   |  ||  | |   ||||   ||    |||| || |||||||| |||||||||||||||||||||| ||||| || ||||||||| ||||||||||||| || |||   || |||||||||||||| || |||||||| || |
gttttttctttctttccttcaccttaatttccaagttacattttggccatcctatctctcctgtgccactgattgcaatctattctgatgttctgtt-tcttccagTTGGACATAATGGACAGGGGCACTGATGCCCGGAACTTTCTGCTGGGAAATGTGATCCCCTTAAAGCTTGGCTATGTTGGTGTCGTCAACCGCAGCCAGC

upper sequence: LOC_Os01g69130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 3
---gtttgaccctggtcttgagttttttgtctggattaaataagcattgtgttcatacca-gtgacccagtttgatcttggcttcacttctattatcttccagCTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAATGTGATTCCATTACGACTAGGCTATGTTGGTGTGGTAAACCGCAGTCAAC
    |||   ||| | ||| | || | || ||  |||   |   |||  | |   | |   |  || || |    ||||| ||    || | || |||||||| |||| ||||||||||||||||| ||||| || ||||||||| ||||||||||||| || |||  ||| |||||||||||||| || |||||||| || |
gtttttttttcctcgccttaatttctatg-ctacatt--ttggccatcctatctctcctgtgccactcaatgcagtcttgtctgatgttgtgtt-tcttccagTTGGATATAATGGACAGGGGCACTGATGCCCGGAACTTTCTGCTGGGAAATGTGATCCCCTTAAAACTTGGCTATGTTGGTGTTGTTAACCGCAGCCAGC

upper sequence: LOC_Os01g69130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------gtttgaccctggtcttgagttttttgtctggattaaat-aagcattgtgttcatacc--agtgacccagttt---gatcttggcttcacttctattatcttccagCTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAATGTGATTCCATTACGACTAGGCTATGTTGGTGTGGTAAACCGCAGTCAAC
                                                                            |      || | |||| ||||   | | ||||   | ||   || | | | |  |  |||| |    | |   | |||| | ||   |    | |   | ||| |||| || ||||| || || |||||||| || || |||||  | |||||||| |||||||||||||| |||||| |||| || |||||| | || ||| 
gtaagctgacttttctattttcttttgtccctactatggcattggtgcttccttcccacattaagaagggttgaaataagttttgcttttgatttttgacttttgattttttcaatttttttatccttttcgaagtgtcttgatcttgagctctttgattggttaacttgaatgtgcagTTGGATATTATGGATAGAGGAACAGATGCGCGGAATTTTCTTCTAGGAAATGTCATTCCATTACGACTTGGCTATATTGGGGTTGTAAACAGGAGCCAAG

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|86826290|gb|CI311113.1|CI311113
EST:     GTTCTCGAACAATTGGTGTTATAACAAAG                         CTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAAT
genomic: GTTCTCGAACAATTGGTGTTATAACAAAGgtttgaccct ... tatcttccagCTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAAT
EST: gi|58654479|gb|CK043159.1|CK043159
EST:     GTTCTCGAACAATTGGTGTTATAACAAAG                         CTGGACATAATGGACAGGTGCACAGATGCTCGTAACTTTCTGTTGGGAAAT
genomic: GTTCTCGAACAATTGGTGTTATAACAAAGgtttgaccct ... tatcttccagCTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAAT
EST: gi|29655723|gb|CB651998.1|CB651998
EST:     GTTCTCGAACAATTGGTGTTATAACAAAG                         CTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAAT
genomic: GTTCTCGAACAATTGGTGTTATAACAAAGgtttgaccct ... tatcttccagCTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttcataccagtgacccagtttgatcttggcttcacttctattatcttccagCTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAATGTGATTCCATTACGACTAGGCTATGTTGGTGTGGTAAACCGCAGTCAAC
                     gtttgat  putative branch site (score: 5)
                                      cttctattatcttcc  putative PPT
                                       ttctattat  TA-rich tract