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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTTGCGTCCGGTAACATACCTAAGTGGTGCACAGGGTTCTGGGAATGACATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatgagtattagctttatctgaaatttatatgttatcccttttcacgtcatgcttaaccttgtcatccttcgattgtatagtttttaaaacttg...

Basic information

species Oryza sativa
transcript LOC_Os04g04254.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G021849_T01 (Zea mays), 5'ss of exon 3
AAGTTGCGTCCGGTAACATACCTAAGTGGTGCACAGGGTTCTGGGAATGACATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatgagtattagctttatctgaaatttatatgttatcccttttcacgtcatgcttaaccttgtcatccttcgattgtatagtttttaaaacttg------
||| ||||||| |||||||| ||||||||| | ||||||||||| |||||||| |||||||| ||||| ||||||||||| || || || ||||| |||||||     |   |||| |||  | |||||| ||      | | |||| |||     |  ||  || | | |       |   | | | | |  || || |      
AAGCTGCGTCCAGTAACATATCTAAGTGGTTCTCAGGGTTCTGGCAATGACATCCCTCATGGATACATTTGGAGTCCTCATCTAGTCCCGAAACCAAAAGgtttgctgtatctattggctagagctgaaagttg-gcaatttaccttgtcat----tcttttcccatattaattccaaagcatgtgggtct-gaatctcgatcttt

upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G007721_T01 (Zea mays), 5'ss of exon 6
AAGTTGCGTCCGGTAACATACCTAAGTGGTGCACAGGGTTCTGGGAATGACATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatgagtattagctttatctgaaatttatatgttatcccttttcacgtcatgcttaaccttgtca-tccttcgattgtatagtttttaaaacttg-----
||| ||||||| |||||||| ||||||||| | ||||||||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| ||||| |||||||    ||   |||| |||  | | | || ||||    | | | ||     |||||  ||  || | | | | |    |   | | | | ||||  ||||     
AAGCTGCGTCCAGTAACATATCTAAGTGGTTCTCAGGGTTCTGGCAATGACATTCCGCATGGATACATTTGGAGTCCTCATCTTGTTCCGAAACCAAAAGgtttgccatatctattggctagagccggaagttatgcaatttacttt-----gtcattttttcccatattagttcccaaagcatgtgggtcttaat-cttgacctt

upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S110_116V6.1 (Physcomitrella patens), 5'ss of exon 10
AAGTTGCGTCCGGTAACATACCTAAGTGGTGCACAGGGTTCTGGGAATGACATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatgagtattagctttatctgaaa--tttatatgttat---cccttttcacgtc---atgctta----accttgt---catccttcgattgtatagtttttaaaacttg---------------------------------------------------------------------
||| | || ||  | || ||| | |||||| | ||||| ||       ||| | |||   || || || ||||||||||| |||||||| ||||||||||||||   |  | |     | | | |||| |  || | ||||| |   |  || | ||| |   ||| | |    |  ||||   ||||     ||   ||  || ||    ||                                                                       
AAGCTACGACCCATCACCTACTTGAGTGGTTCTCAGGGCTCCATCGCCGACTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAGgttcg-aactattcacctcctcacctgatacgttcaaatgtttttgacaattgttacgccgatatgttgattgcaaattgtgcacatcagataatccgattattcttgcgtctgattttattagtttgtgacaattgagtgctgaaattatcaggattcttacgaggacgtctcacttttacag

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|13165000|gb|AU173797.1|AU173797
EST:     CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAG                         ATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
genomic: CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatg ... tctgttgcagATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
EST: gi|42793914|gb|AB117813.1|AB117813
EST:     CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAG                         ATTGGGGCCCCAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
genomic: CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatg ... tctgttgcagATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
EST: gi|58670931|gb|CK059617.1|CK059617
EST:     CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAG                         ATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
genomic: CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatg ... tctgttgcagATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT