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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGACATCAGTTGGTATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatgctataattcctcactcgtggttgaattgtcaagaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaaccagtcagattttttgtgctaatgatgtgttccattgtgtgtttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g40090.4
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G823629_T03 (Zea mays), 5'ss of exon 1
GCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGACATCAGTTGGTATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaaga-catgctataattcctcactcgtggttgaattgtcaagaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaa--ccagtcagatt-ttttgtgctaatgatgtgttccattgtgtgtttgtgcag
||||  || |||||||| |||||||||||||| || || ||||| ||||||||||||||||||||||| |  |||||||| || ||||| |||||||||||||||| |||||   |  || ||| || |   || ||        ||||||  | | | ||     |   |   |     |||   |||||   |||||||| |||   ||||| | || | ||||||||||  |||   | |   | || |  | |||
GCAGCACTAGATGCTGGCGCATGGATGTTCAATGTCGTCACATCTGTTGGTATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcatgcccaa--tcttcattcctaactgcat-----gcgatgcctgattcacgcgcgccttctttt-ctatctaaaagtaaactactattgtgcagaaaaattcagtctgcttgtcttgtgctaatt-tgttcactaccttttgctcctacag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G089630_T03 (Zea mays), 5'ss of exon 2
GCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGACATCAGTTGGTATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatgctataattcctcactc--gtggttgaat-tgtcaagaatgccttgtccgcacg---------tcttatggatagttggacta----------------------aaccgaactatcgttgtgcagcaaaccagtcagatt-ttttgtgctaatgatgtgttccattgtgtgtttgtgcag
||||  || || ||||| |||||||||||||| || || ||||| ||||||||||||||||||||||| || |||||||| || |||||||||||||| ||||||||       ||    ||  ||   |    |  |  |   |  ||||||  | | | ||         |  | |  | |  |  ||||                      ||   |||||| | ||||||   |||||||| |||  | || | |||||  |||   |   | | || ||   |||
GCAGCACTAGACGCTGGCGCATGGATGTTCAATGTCGTCACATCCGTTGGTATCATCATGGTCAACAAAGCCTTAATGGCGACGCATGGTTTTAGTTTCGgtaagaccgtgcccaacctttcgttcctataaccgcgtacgagtacgatgcctaattcacccgcgtctttgtttctgtctaaaactaaactacgattttgctgagaaccagtctaattaaactatggctgtgcatagaaccagtctgatcgtcttatactaatt-tgttcgctgctatttgcttcgacag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G08700.1 (Glycine max), 5'ss of exon 2
GCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGACATCAGTTGGTATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatgctat--aattcctcactcg-tggttgaattgtcaa-gaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaaccagtcagattttttgtgctaatgatgtgttccattgtgtgtttgtgcag
|| |   ||||||| |  |||||||||||||| ||||| ||||| ||||| |||||||| || ||||| || || |||||| |  |||| || ||||||||||| |    ||||  |||| || | | |  | ||   || |     ||| || | | ||  | |  | ||    |||    |      | || |   ||||      |   |||   |  |   |||                               
GCTGCCGTGGATGCAGCTGCATGGATGTTCAATGTTGTTACATCTGTTGGAATCATCATTGTAAACAAAGCTTTGATGGCCTCTTATGGCTTCAGTTTTGgtaa-attccctattcaatttcttaatggacgtttctgttattggcaaattccctatacgatcatgctctgat--gttaattt---tttatcttttaatgtg------atttgtctattactgcttgcag-----------------------------

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G27820.1 (Glycine max), 5'ss of exon 1
GCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGACATCAGTTGGTATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaaga-catgctataattcctcactcgtggttgaattgtcaaga----atgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaaccagtcagattttttgtgctaatgatgtgttccattgtgtgtttgtgcag
|| |   ||||||| |  |||||||||||||| ||||| ||||| ||||| |||||||| || ||||| || || ||||||||  |||| || |||||||||||   | |  |  |||| || | |     ||   || |    |      | ||| ||| || ||  |||       ||  |     |  |   |  || |      | |   | |  |  ||||| ||| |  ||  | |          ||   |||
GCTGCTATGGATGCAGCTGCATGGATGTTCAATGTTGTTACATCTGTTGGAATCATCATTGTAAACAAAGCTTTGATGGCCACTTATGGCTTCAGTTTTGgtaaattccttattcaatttcttaatgacatttctgttattggtatactgagtcttttcc-caggtagtatatgatcatgatcatgctctgatgttaattttttttttatcttttaatgtgatttgt-ctattactgcttgcggccacaacatta-acag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 2
GCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGACATCAGTTGGTATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatgcta--taattcctcactcgtggttgaattgtcaagaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaaccagtcagattttttgtgctaatgatgtgttccattgtgtgtttgtgcag
|||    | |||||||  || ||||||||||| ||||| || || |||||||||||||| || || || || |||||||| ||  |||| ||||| |||||||   | |  |    ||  ||| | |     |   ||  |||  |||   |||||   |  | ||     |   || |                                                                              
GCAACATTAGATGCTGCTGCTTGGATGTTCAATGTTGTTACTTCTGTTGGTATCATCATTGTTAATAAAGCTTTAATGGCTACTTATGGCTTTAGCTTTGgtacttcttcttcatcaaaaccttatttacaatcatatcttca--aattatttgtcta-atattttcaatttcaatgcag-----------------------------------------------------------------------------

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
GCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGACATCAGTTGGTATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatgctataattcctcactcgt--ggttgaattgtcaagaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaaccagtcagattttttgtgctaatgatgtgttccattgtgtgtttgtgcag
|||    | |||||||  |||||||||||||| ||||| || || ||||| ||||| ||||||||||| || |||||||| ||| |||| || |||||||||| | |   | || | |    || |    | || |||          |||||      || || || | ||||||   |||||   |       || ||||                                                       
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccctc-atgactatcaacccacacgctttaatcaatttatcagcctttatattac-tcatacg-atagtt---ctaaatgcattgtgtcttatgcatttc---------------------------------------------------

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 5'ss of exon 1
GCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGACATCAGTTGGTATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatgctataattcctcactcgtggttgaattgtcaagaatgccttgtccgcacgtcttatggata-gttggactaaaccgaactatcgttgtgcagcaaaccagtcagattttttgtgctaatgatgtgttccattgtgtgtttgtgcag
||||  || ||||| |  |||||||||||||| ||||| || || ||||| || ||| | |||||||| ||||||||||| ||| |||| || |||||||||||  | |     || |       |||  ||   |||   |   |   ||| | |    | || |  | | |   |  |  |   || | ||  |    |                                                       
GCAGCACTAGATGCAGCCGCATGGATGTTCAATGTTGTCACTTCTGTTGGGATTATCCTTGTCAACAAAGCATTAATGGCTACATATGGATTCAGTTTTGgtaattcttttctaaagtaaatttgcgttttttctttgattaatttcttttgcctgtgtatattttttacatgcatgtgtggat--aattctcacttcttaa------------------------------------------------------

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|29639689|gb|CB644698.1|CB644698
EST:     TATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTG                         CTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAG
genomic: TATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatg ... gtttgtgcagCTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAG
EST: gi|88398814|gb|CI601150.1|CI601150
EST:     TATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTATTTTTG                         CTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAG
genomic: TATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatg ... gtttgtgcagCTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAG