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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaaaaacacatttggttttatattatgtttttatattttaagccaagtccaaaacctgtttctgtttctgattttccttacttactttgctttatattattgtttgtcgtagATCGGATGTATTAGGCCAGTTTATGCCTTTGGTTGGTATAGATTGGTCACAAACAGGTGTTACACATTTGTTTTCGGCTGTAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G42870.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G04060.1 (Glycine max), 3'ss of exon 9
gtaaagaaaaacacatttggttttatattatgtttttatattttaagccaagtccaaaacctgtttctgtttctgattttccttacttactttgctttatattattgtttgtcgtagATCGGATGTATTAGGCCAGTTTATGCCTTTGGTTGGTATAGATTGGTCACAAACAGGTGTTACACATTTGTTTTCGGCTGTAAAG
    |  | |   ||| |  |||  |  | |  | |||| ||  ||   |  || ||  |  || |    || | ||||       |||  ||| || || |         |   || || |||||  | || ||||| ||||||||||||||||| || |||||||| ||||||||| ||||||| || || ||| | |||
-ccgaatagagtccatgtattttgcttctcttctgttattttcaaa---agatctaactctagtatgaaattgtaatttct-----ttatcttgtttcatgtc--------ttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCTATCAAG

upper sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G04230.1 (Glycine max), 3'ss of exon 10
gtaaagaaaaacacatttggttttatattatgtttttatattttaagccaagtccaaaacctgtttctgtttctgattttccttacttactttgctttatattattgtttgtcgtagATCGGATGTATTAGGCCAGTTTATGCCTTTGGTTGGTATAGATTGGTCACAAACAGGTGTTACACATTTGTTTTCGGCTGTAAAG
           |  | | |  |  || |  | | ||| | || |  |  |  | |||||  |    ||   |||  | |    |  | | ||   ||| |  | |  ||| |   || || |||||  | || ||||| ||||||||||||||||| || |||||||| ||||||||| ||||||| || || ||  | |||
-----------cctaatagagtccatgtcttttgtttctcttct--gttattttcaaaagat----ctaactctagtatgaaattgtaatttctttttcttgtttcatttcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCAATCAAG

upper sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------gtaaagaaaaacacatttggttttatattatgttt-ttatattttaagccaagtccaaaacctgtt-----tctgtttctgattttccttacttactttgctttatattat-tgtttgtcgtagATCGGATGTATTAGGCCAGTTTATGCCTTTGGTTGGTATAGATTGGTCACAAACAGGTGTTACACATTTGTTTTCGGCTGTAAAG
                                             |||    | |     || | ||  || | |  | | ||||| |||  |   |  | |  ||| ||      | | ||  || ||   |  |  |   |   ||| | ||   |  || |   || || |||||  |||| ||||| |||||| |||||||  ||||||||||||| ||||||||  ||||| | ||||| ||| | |||
gtaagggtactcaaatctttttctaaggttaaaaattgataccttgtatgttagatgtttttggattgaatttcacttctattatagtttg-gttgatacaagcaccagtagatcatatattcttgcttggacccatctgactccttttgtcttgcattcttattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG

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|164161677|gb|ES140203.1|ES140203
EST:     CAGATGTAGATGGTACCATCACAAG                         ATCGGATGTATTAGGGCAGTTTATGCCTTTGGTTGGTA
genomic: CAGATGTAGATGGTACCATCACAAGgtaaagaaaa ... tttgtcgtagATCGGATGTATTAGGCCAGTTTATGCCTTTGGTTGGTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctgtttctgattttccttacttactttgctttatattattgtttgtcgtagATCGGATGTATTAGGCCAGTTTATGCCTTTGGTTGGTATAGATTGGTCACAAACAGGTGTTACACATTTGTTTTCGGCTGTAAAG
                     tacttac  putative branch site (score: 1)
                                 tttatattattgtttg  TA-rich tract