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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgttcagcttttgtttgctccgtgttatttctgtaatcaagatgctattcatatgtttttgctttcgagtatggatgggttgatgcgacctacatcactcacatcattgaatttgtttatgcagCTTCTGTTATTTGGGGGACATGGAACTGGTGGATGGCTGAGTCGTTATGATGTTTACTATAATGATACTATAATTTTGGACAGAG

Basic information

species Arabidopsis thaliana
transcript AT2G36360.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G36360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g61950.1 (Oryza sativa), 3'ss of exon 9
gtatgtgtgttcagcttttgtttgctccgtgttatttctgtaatcaagatgctattcatatgtttttgctttcgagtatggatgggttgatgcg-acctacatcactcacatcattgaatttgtttatgcagCTTCTGTTATTTGGGGGACATGGAACTGGTGGATGGCTGAGTCGTTATGATGTTTACTATAATGATACTATAATTTTGGACAGAG
                                |  | ||| ||  |     |  |||      ||||| | || |  |    |   |   |||| |    ||| ||| ||| |  |  || | ||  |  ||||  || | ||||| ||||||||||||||||| ||||| ||| | |||||||| ||||| |||||   ||| ||||| ||||| |
------------------------------tcttctcctggaactatccatcagttctagacattttgttgtccaa-acttttaattcattgcgcaatagcattactaacaaccatatatcttttggt-tagCTCTTGCTGTTTGGAGGACATGGAACTGGTGGTTGGCTAAGTAGGTATGATGTGTACTACAATGAATGTATTATTTTAGACAGGG

upper sequence: AT2G36360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G351160_T01 (Zea mays), 3'ss of exon 9
gtatgtgtgttcagcttttgtttgctccgtgt-tatttctgtaatcaagatgctattcatatgtttttgctttcgagtatggatgggttgatgcgacctacatcactcacatcattgaatttgtttatgcagCTTCTGTTATTTGGGGGACATGGAACTGGTGGATGGCTGAGTCGTTATGATGTTTACTATAATGATACTATAATTTTGGACAGAG
                            || | ||| |    ||   |||| || || |  | ||||         || | ||| |  || | |     ||   |     ||      || | |||   |||||  || | ||||| ||||||||||||||||| ||||| ||| | |||||||| |||||||||||    || ||||| ||||| |
---------------------------agtttatatattcagaagttagattctgttgagtttttttcatgcaaaggtcttgattgcatggt-cagttaactgaagatgtat----atatcttttttgtcagCTCTTGCTGTTTGGAGGACATGGAACTGGTGGTTGGCTAAGTAGATATGATGTGTACTATAATGAATGCATTATTTTAGACAGGG

upper sequence: AT2G36360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G32900.1 (Glycine max), 3'ss of exon 9
gtatgtgtgttcagcttttgtttgctccgtgttatttctgtaatcaagatgctattcatatgtttttgctttcgagtatggatgggttgatgcgacctacatcactcacatcattg--aatttgtttatgcagCTTCTGTTATTTGGGGGACATGGAACTGGTGGATGGCTGAGTCGTTATGATGTTTACTATAATGATACTATAATTTTGGACAGAG
                         ||  |  |   ||  | |||| ||    ||  |||  |||    |||          ||   |  ||  |  ||  |   |   ||  |||       |||| |  || |  || | ||||| || ||||| |||||||||||| |||||||||||||| | || |||||||||   || || || |||||||
------------------------ttcaatacttaatccttcatcatga----atgtataaatttaccattttagcc-----tgaaatcctgtcatttatttattttttatttttgttggagggtttttatagTTGTTGATGTTTGGAGGGCATGGGACTGGTGGATGGTTGAGTCGTTATGATATCTATTATAATGATTGCATTATATTAGACAGAG

upper sequence: AT2G36360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv13s0074g00620.t01 (Vitis vinifera), 3'ss of exon 10
gtatgtgtgttcagcttttgtttgctccgtgttatttctgtaatcaagatgctattcatatgtttttgctttcgagtatggatgggttgatgcgacctacatcactcacatcattgaatttgtttatgcagCTTCTGTTATTTGGGGGACATGGAACTGGTGGATGGCTGAGTCGTTATGATGTTTACTATAATGATACTATAATTTTGGACAGAG
                           |||||  |||   ||       || | || || |     ||  | |||   |   |    ||        ||| | ||| | |  ||    | ||| | |||||||  ||||||||||||| ||||| |||||||| ||| |||||||||||||  ||||||| |||||    ||  ||||||| || |
-------------------------ctcgtgtc-tttgcatagcttc--tgatttttat-tcccactgtgtccgaacttcctttttctgggattgagtacctgactgagaagatc--ttgtgtctttgcagCTCTTGTTATTTGGGGGGCATGGGACTGGTGGTTGGTTGAGTCGTTATGACATTTACTACAATGAATGCATTGTTTTGGATAGGG

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|125211166|gb|EL226120.1|EL226120
EST:     AAGCACCATCATCTCGATGTGGTCATACAGTTACATCTGGAGGACATTAT                         CTTCTGTTATTTGGGGGACATGGAACTGGTGGATGG
genomic: AAGCACCATCATCTCGATGTGGTCATACAGTTACATCTGGAGGACATTATgtatgtgtgt ... gtttatgcagCTTCTGTTATTTGGGGGACATGGAACTGGTGGATGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggatgggttgatgcgacctacatcactcacatcattgaatttgtttatgcagCTTCTGTTATTTGGGGGACATGGAACTGGTGGATGGCTGAGTCGTTATGATGTTTACTATAATGATACTATAATTTTGGACAGAG
                          cactcac  putative branch site (score: 2)
                                          tttgttt  putative PPT
                                    attgaatttgtttat  TA-rich tract