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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATATTCTCATCCTCTTCTTCTCTTGGCTCCTCGTTCTCTCCGTCTTCCATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcccgatctcctccgatccaatttcgaaattgttggtttctagatttgaatttttgagtttttttgttttctag

Basic information

species Arabidopsis thaliana
transcript AT5G42000.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42000.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os02g45180.1 (Oryza sativa), 5'ss of exon 1
TTATATTCTCATCCTCTTCTTCTCTTGGCTCCTCGTTCTCTCCGTCTTCCATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcccgatc----------tcctccgatc----caatt----tcgaaattgttggtttctagatt-tgaatttttgagtttttttgttttctag
 || ||   ||||||||||||||| ||||||||||| ||||||||||||   ||  | || ||||| || |||||| | ||  |||||   || ||| | ||| |  ||||   |          ||||||  ||    | |||    |||  || || |   ||    || ||| |            ||| ||| || 
CTACATCTGCATCCTCTTCTTCTCCTGGCTCCTCGTCCTCTCCGTCTTCGGCTGCACGCCCGGCATGGCCTGGACCGTCGTCAATCTCTTCCACTTCGCGgtaatcctccccgccttgcgccacgtcctccattcattaccattcccgtcgtcatcgtcgtcgtccgttttgtgagtgccactacgcgcttgctttgtaa

upper sequence: AT5G42000.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os04g47970.1 (Oryza sativa), 5'ss of exon 1
TTATATTCTCATCCTCTTCTTCTCTTGGCTCCTCGTTCTCTCCGTCTTCCATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcccgatctcctccgatccaatttcgaaattg---ttggtttctagatttgaatttttgagtttttttgttttctag------------------
 || || ||||||||||||||||| ||||| ||||| ||||||||||||   ||  | || ||||| || |||||  | ||  | ||||| || ||| | |||     |||  ||     || | |    | ||| | |   | || |    |    |  || |||     ||| | |  || |                  
CTACATCCTCATCCTCTTCTTCTCCTGGCTGCTCGTCCTCTCCGTCTTCGGCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggacccc--tccttctcgcttctccctggaattcggattaggatcgagggccagcgttcttggcaagtttagctcgctcgctcgttcgtatcatcagg

upper sequence: AT5G42000.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G151009_T01 (Zea mays), 5'ss of exon 1
TTATATTCTCATCCTCTTCTTCTCTTGGCTCCTCGTTCTCTCCGTCTTCCATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcccgatctcctccgatccaatttcgaaattgttggtttctagatt--tgaatttttg-agtttttttgttttctag-------------------
 || ||  ||||| |||||||||| ||||||||||| |||||||||||    ||  | ||||||| ||| |||||| | ||  | |||   || ||| | |||     | |  ||   | |  || | |  | |   |       ||  |  |  | ||||  ||  |  ||    ||| ||                     
CTACATCATCATCGTCTTCTTCTCCTGGCTCCTCGTCCTCTCCGTCTTTGGCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcctctttcgatttctctcaagtcccaagcctccc---ctccggcctcgtaaattcgtgcggggttcccatttgctgttgaaattttgacccggagt

upper sequence: AT5G42000.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G114911_T02 (Zea mays), 5'ss of exon 1
TTATATTCTCATCCTCTTCTTCTCTTGGCTCCTCGTTCTCTCCGTCTTCCATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcccgatctcctccgatccaatttcgaaattgttggtttctagatttgaatttttgagtt---tttttgttttctag-------------------
 || || |||||  |||||||||| ||||||||||| ||||||||||||   ||  | ||||||| ||| |||||| | ||  | |||   || ||| | |||     | |  ||   |||   |||| | | ||          ||  |  | | || |  | |     ||    ||| ||                     
CTACATCCTCATTGTCTTCTTCTCCTGGCTCCTCGTCCTCTCCGTCTTCGGCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcctct-tccgttccttcccaagtcccaagcctcc--cctcccgcctcgtatgtgcgtgcggggttcccatttgctgctgaattgtgaccctgggtg

upper sequence: AT5G42000.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G044720_T01 (Zea mays), 5'ss of exon 1
TTATATTCTCATCCTCTTCTTCTCTTGGCTCCTCGTTCTCTCCGTCTTCCATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgt-attattcccgatctcctccgatccaatttcgaaattgttggtttctagatttgaatttttgagtttttttgttttctag------------------
 || || ||| | ||||||||| ||||||||||||| ||||||||||    ||| || || ||    || |||||  | ||  | ||||| || ||| |||| | |   | |  |||  ||||  || | | |       ||  |     | ||||  |    | | ||  | |     | |                  
CTACATCCTCCTGCTCTTCTTCGCTTGGCTCCTCGTCCTCTCCGTCTCTGGTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttcccaccctctattccgtccccagtccctcgccctttctactggggtttgcttacgagcggttgctcgcgcgatcgacttctgattttgcgcat

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|125261111|gb|EL275196.1|EL275196
EST:     ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACC                         GTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTT
genomic: ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcc ... tgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTT
EST: gi|124906820|gb|EH980900.1|EH980900
EST:     ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACC                         GTCACGTATCATTCCTTCCAT
genomic: ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcc ... tgttttctagGTCACGTATCATTCCTTCCAT
EST: gi|125225328|gb|EL239413.1|EL239413
EST:     CTCGCTCATTTCACC                         GTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGAT
genomic: CTCGCTCATTTCACCgtattattcc ... tgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGAT
EST: gi|125178960|gb|EL197081.1|EL197081
EST:     ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACC                         GTCACGTATCATTCCTTCCATTGGAAGAAGGG
genomic: ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcc ... tgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGG