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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactattaacttacccttgtcttcttttacattttagttaccgatgctaatattatttacttgtttttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC

Basic information

species Arabidopsis thaliana
transcript AT1G77760.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G77760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
-----------------------gtaaac-tattaacttacccttgtcttcttttacattttagttaccgatgctaatattatttacttgtttttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC
                          |||  | |     |  |     || ||  |  |||  | |    |      | || |||  |||  ||   | ||||||||||||| ||||| || ||||| || |||||||| || |||||||||||||| || || || || ||||  ||| |  | || || |||||  | ||
gtaattaaccaaccatatcttcctcgaacgcactgcacgagacacacattgttgcatctttgtgatcttaacttgtgtgttttttttttggattatgtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC

upper sequence: AT1G77760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G568636_T01 (Zea mays), 3'ss of exon 1
gtaaactattaacttacccttgtcttctt-ttac---attttagttaccgatg-ctaatattat--ttacttgtttttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC
||||  ||  |  | |   ||   || ||  |||   |    |   |  |||| || |  ||    || |   |  |||   |||| |||||||| ||||| || ||||| ||||||||||| || |||||||||||||| || || || || ||||  |||||  | || || ||     | ||
gtaa-ttagcagttcatgtttaatttattactactcaagcaaaaaaaatgatgtctgactttgctattgcaaatgattga-gcagCGTGGTGGTACAAGCCGGAGTACATCATCAACGAGCTGAACATAAACTCGGTGATAACGACGCCGGGGCACGACGAGATCCTGCCCATCAACAGCATTAC

upper sequence: AT1G77760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G076723_T01 (Zea mays), 3'ss of exon 1
gtaaactattaacttacccttgtcttct-----tttacattttagttaccgatgctaatattattt---acttgtttttgtta------cagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC
||||    |     |    |||| | ||     |    |    ||  | | |    ||    ||||    |||| |  ||  |      |||| |||||||| ||||| || ||||| ||||||||||| || |||||||||||||| || || || || ||||  |||||  | || || || |   ||||
gtaactagtgtttgtttgtttgtttactacggatcggaagcaaagcaagcaagcgaaacgggattttgatcttgctgctgcaaaatgagcagCGTGGTGGTACAAGCCGGAGTACATCATCAACGAGCTGAACATAAACTCGGTGATAACGACGCCGGGGCACGACGAGATCCTGCCCATCAACGGCATCAC

upper sequence: AT1G77760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------------------------gtaaactattaacttacccttgtcttcttttacattttagttaccgatgctaatattatttactt--gt-ttttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC
                                                                                    | | | |  ||  ||  |  ||   | |     |||| |   || ||   ||||    |||  ||  || | |  ||  || ||||||||| ||||| |||||||| ||||||||| | ||||||||||| ||||| || || ||| ||||||  ||||| || || || ||  |||  ||
gtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtgagatttagataatttcatggacagaaattaatgacgttttttttggtgtctccttgtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC

upper sequence: AT1G77760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 1
--------gtaaactattaacttacccttgtcttcttttacattttagttaccgatgct-----aatattatttact-tgttt-----ttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC
         ||  |  ||  ||||   || |  |||  || ||| || |   |  || |     |||| | ||| || |||||     || ||  |||||||||||| ||||| || || || |||||||||||||| |||||||| ||||| || || ||| | ||||  ||||| || || || ||  |||  ||
gtattctactattcccttttcttatttttttgctctcataaattctaatagactttgattataaaataatgttttctctgtttcaatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC

upper sequence: AT1G77760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 1
---------------------gtaaactattaacttacccttgtcttcttt-----tacattttagttaccgatgctaatattatttacttgtttttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC
                      || |  ||     | ||   |  || |||      |||  ||| ||||   |  | ||||| ||    |||   ||   ||| ||||||||||||||| ||||| || ||||||||| | || |||||||| ||||| || || ||  |||||   ||||| || || || ||  |||  ||
caacttagagatgtgtgtaacatataacatgtttcttccaaggaattttttcatggcacaaattaattacatgt-ttgatattcttggtgtgtccctg---cagGTTGGTGGTATAAGCCGGAATATATCATCAACGAGTTGAACATAAACTCAGTGATAACGACGCCGTGTCACCAGGAGATCTTGCCCATCAACTCATGGAC

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|125032829|gb|EL105098.1|EL105098
EST:     AGCTGGCAAATTCCGAAG                         CTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTACG
genomic: AGCTGGCAAATTCCGAAGgtaaactatt ... tttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACT-CG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttttacattttagttaccgatgctaatattatttacttgtttttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC
                        tgctaat  putative branch site (score: 2)
                                       cttgttttt  putative PPT
                           taatattatttacttg  TA-rich tract