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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatttttgcttctttctttctttctttctttctttgtaggtttgttttgtcgtagtatctgattgaatttgatctgtgcagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G59900.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 1
gtaagcatttttgcttctttctt---tctttctttctt-----tctttgtaggtttgttt--tgtcgtagtatct-gattgaatttgatctgtgcagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG
|| ||    | |||  ||||      || |  || | |     | | ||   |||  |||  |||  ||  |||| ||||  ||||    ||||||||||| |||||||| ||||| ||||| || || ||||| ||  | ||||||||||||||||||||||| |||||| | |||
gtgagttcctgtgccgcttttgggaatcatgattgcatcgtgatatctgcttgttcatttgatgtgatatgatcttgattcgatttcccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACAAGCGTGGTGATTATGTGCCTGGATTGAAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G140150_T01 (Zea mays), 3'ss of exon 1
----------------------gtaagcatttttgcttctttctttctttctttctttctttgtaggtttgttttgtcgtagtatctgattgaatttgatctgtgcagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG
                      | || |    || | || |       |  ||   ||| |  |  |     | || |||  | |  | |||| ||   | |||  |||||| |||||||| || |||||||| || || ||||||||  |||||||||||||||| || ||||| |||||| | |||
gtgagttcgtgcatcagttccgggaaacggggttacatcgtgaaaatctgattg--ttcatcatgaga--aatatgacgtgatctgggtttgatttctgt-tgtatagATGGTATGGGAACAGCGGAATGGAGGGCAGCGAAGAGTCCTGCTTACTACAAGCGTGGCGACTATGTGCCTGGATTGAAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 1
gtaagcatttttgcttctttctttctttctt-----tctttctttgtaggtttgttttgtcg---tagtatctgattga----atttgatctgtg---cagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG
 | |   ||| | ||| | |   |  || ||     |  |  |||| |       ||||| |   | |  |  |||| |     |||| | ||||   ||||||||||||| || ||||| |||||||| |||||||||||  |||| ||||||||||| ||||||||||||||| | |||
-ttattttttattcttttgtaactgcttattgaaaataataatttgaaaagggactttgttgatttgggtttggattaatttggtttggtttgtgggacagATGGAATGGGGACAGCTGAGTGGAGAGCTGCTAAGAGTCCTGCTTATTACAAGCGTGGGGATTATGTTCCTGGATTGAAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 1
gtaagcatttttgcttctttctttctttctt-------tctttctttgtaggtttgttttgtcgtagtatctgattga----atttgatctgtg---cagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG
|| |   ||||  ||  |     |  || ||       |  | |     ||| || | |||   | |  |  |||| |     |||| | ||||   ||||||||||||| || ||||| |||||||| |||||||||||   ||| ||||||||||| ||||||||||||||| | |||
gttatttttttctctcttccaagtgcttattggaaaaatgatccaaacaaggcttttgttgatttgggtttcgattaatttggtttggtttgtgggacagATGGAATGGGGACAGCTGAGTGGAGAGCTGCTAAGAGTCCTAGTTATTACAAGCGTGGGGATTATGTTCCTGGATTGAAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 1
gtaagcatttttgc-ttctttctttctttctttc---tttctttgtaggtttgtttt-gtcgtagtatctgattgaatttgatctgtgcagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG
||||| | |   |  |||| |  |  ||    ||    |  | |||  ||| | ||  ||   | | |||  ||||| ||  | || |||||||| ||||| || ||||| |||||||| || ||||||||| | || |||||||| || || |||||||||||  | |||
gtaagaaatgagggattctatagtaattggaatcgggctgttgtgtgagttcgattgagtttcaatttct--ttgaacttcttttg-gcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 1
gtaagcatttttgcttctttctttctttctttctttctttgtaggtttgttttgtcgtagtatctgattgaatttgatctgtgcagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG
||||| | |   |  | ||   |  ||    |       ||   | |||| |     ||   | |  ||||| ||  | || |||||||||||||| || || || |||||||| || ||||||||| | || ||||||||||| || ||||| |||||  | |||
gtaagaaatgagggattttatataattggaat-------tgggtggttgtgtgagtttaa-gtttatttgaacttt-tatgggcagATGGAATGGGTACGGCAGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAG

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|164057907|gb|EL992621.1|EL992621
EST:     TTCTGCTATTTGGGATTTGCCTGCAATTTTGGTCTGCGAGAACAATCACT                         ATGGAATGGGAACT
genomic: TTCTGCTCTTTGGGATTTGCCTGCAATTTTGGTCTGCGAGAACAATCACTgtaagcattt ... atctgtgcagATGGAATGGGAACT
EST: gi|125192332|gb|EL207286.1|EL207286
EST:     TTCTGCTCTTTGGGATTTGCCTGCAATTTTGGTCTGCGAGAACAATCACT                         ATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCAT
genomic: TTCTGCTCTTTGGGATTTGCCTGCAATTTTGGTCTGCGAGAACAATCACTgtaagcattt ... atctgtgcagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCAT
EST: gi|124920991|gb|EH994655.1|EH994655
EST:     CAATTTTGGTCTGCGAGAACAATCACT                         ATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACT
genomic: CAATTTTGGTCTGCGAGAACAATCACTgtaagcattt ... atctgtgcagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctttgtaggtttgttttgtcgtagtatctgattgaatttgatctgtgcagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG
                                   attgaattt  TA-rich tract