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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtggatttgagaaagttgtgtatgtgttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG

Basic information

species Arabidopsis thaliana
transcript AT2G18750.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 2
gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtggatttgagaaagttgtgtatgtgt--tattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG
                                                   | ||| | |  |   | | |  ||| |      |||| | | |||| || |   ||| | |  |  |   |||   |  |     |||     ||||||||||| |||||||||||  | ||| |||||||||| |||| ||||||||| ||  |||| || ||||||||  |||| 
---------------------------------------------------taaattttttttgtgtatatccttgaaattgcaaaaatatgtttgt-atcttagttgctcgatttagaggttgctcacttaacaaatgacacatattgcagTGTCATTGTGGAAGCTCTTAAGGTGGATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtgg-atttgagaaagttgtgtatgtgttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG
                                                  |||  | | | |||  | |  || |  |    ||| ||   |    ||  || | ||| |  |||||     ||      | |  |  | | |   |||||||| ||||| ||||| || ||| |||||||| | ||||||||||| || ||  ||||||| ||||||||  |||||
------------------------------------------------ccttgcgtgt-tcattactgtaaagctcaacatgtgagaaggtga--attgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtggatttgagaaagttgtgtatgtgttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG
                                       |       ||| |   |  |   || ||||  |   |||| ||| | ||||   |        | |||   |   |||  ||      ||  | | ||| |     |||||||| ||||| ||||| || |||||||||||| | |||||||| || || ||  ||||||| ||||||||  |||| 
---------------------------------------tggctctcttgcttgtttggcgttttattttaa--cgtattaataacaaaataatgacctatcacatt--ctagttgtaaat------aatctctctatctacc-ctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtgg-atttgagaaagttgtgtatgtg-ttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG
                                         || | ||| |   || | | ||| |||   | |  | |   ||         || | || |||||| |||||  ||   || | |   | |  || |  |  || | |||||||||||||||||||  ||||| |||| ||||| |||| |||||| || ||||| ||||| ||||||||  |||| 
-----------------------------------------atagggtttt---atttcttattaattataattcatctagttgt--------ttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtggatt-tgagaaagttgtgtatgtgttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG
                                                    |||  | | |||  ||  || |  ||         |   | || | || |||||| |||||  ||    | | |   | |  |  |  | || |||||||||||||||||||||  | ||| |||| ||||| |||| |||||| || ||||| ||||| ||||||||  |||| 
-------------------------------------------------aaagaagattttatttcttattaatcata-atccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatatt-ttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

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|164229711|gb|ES160746.1|ES160746
EST:     AAAAGGCCAGCTCTTGCAAG                         TGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTC
genomic: AAAAGGCCAGCTCTTGCAAGgtaatttgtg ... gttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTC
EST: gi|124866956|gb|EH951393.1|EH951393
EST:     AGCCTGAGCGTAAAAGGCCAGCTCTTGCAAG                         TGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGG
genomic: AGCCTGAGCGTAAAAGGCCAGCTCTTGCAAGgtaatttgtg ... gttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatgtatattgattgtctgtggatttgagaaagttgtgtatgtgttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG
        tattgat  putative branch site (score: 3)
      tatattgatt  TA-rich tract