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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaattcactcatgaactctgttcaatactcctcttccttgataacatgttcatctcggtaatgagacttttataccttgtaatttgtatttgcagGGATAGAGAACACTTTACCAATTGATCCATGGCATATTGGAGGTCCAGTCATCAAAGGATTTGGCCGTGGCTCTAAAGTACTCGGAATCCCCACCG

Basic information

species Arabidopsis thaliana
transcript AT4G21470.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21470.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g32730.1 (Oryza sativa), 3'ss of exon 7
gtaaaaattcactcatgaactctgttcaatactcctcttccttgataacatgttcatctcggtaatgagacttttataccttgtaatttgtatttgcagGGATAGAGAACACTTTACCAATTGATCCATGGCATATTGGAGGTCCAGTCATCAAAGGATTTGGCCGTGGCTCTAAAGTACTCGGAATCCCCACCG
          |  |   ||||||    | |||| || ||     ||    ||  |||||          |||| | |||      |||| | | ||||||||| ||  | || |||||||| || ||||||  |||||| || || || || ||||||||||||||||| ||||||||||| ||||| || || |
--------gtatgctctaactcttgggactacttctgttagaaaat--tctgggcatcttta-------acttatctactgacatatttct-tatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG

upper sequence: AT4G21470.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G027115_T01 (Zea mays), 3'ss of exon 8
gtaaaaattcactcatgaactctgttcaatactcctcttccttgataacatgt--tcatctcggtaatgagacttttataccttgtaatttgtatttgcagGGATAGAGAACACTTTACCAATTGATCCATGGCATATTGGAGGTCCAGTCATCAAAGGATTTGGCCGTGGCTCTAAAGTACTCGGAATCCCCACCG
|||       | || ||| ||    || |||||  | ||| |||| || |     | || | |||  | || ||| | |  |    ||| ||  | ||||||||| ||    || |||||||| || ||||||  |||||| || || || |||||||||||||||||||| ||||||||||| ||||| || || |
gtatgttcaaagtcttgagcttc--tctatacttttgttcattgagaagagaacattatgtgggttttaag-cttatctgtcgataaatgtgc-tgtgcagGGATTGAAGGTACCTTACCAATAGAACCATGGTTTATTGGTGGGCCTGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAG

upper sequence: AT4G21470.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G027115_T02 (Zea mays), 3'ss of exon 8
gtaaaaattcactcatgaactctgttcaatactcctcttccttgataacatg--ttcatctcggtaatgagacttttataccttgtaatttgtatttgcagGGATAGAGAACACTTTACCAATTGATCCATGGCATATTGGAGGTCCAGTCATCAAAGGATTTGGCCGTGGCTCTAAAGTACTCGGAATCCCCACCG----
|||       | || ||| ||    || |||||  | ||| |||| || |     | || | |||  | || ||| | |  |    ||| ||  | ||||||||| ||    || |||||||| || ||||||  |||||| || || || |||||||||||||||||||| ||||||||||| ||||| || || |    
gtatgttcaaagtcttgagcttc--tctatacttttgttcattgagaagagaacattatgtgggttttaag-cttatctgtcgataaatgtgc-tgtgcagGGATTGAAGGTACCTTACCAATAGAACCATGGTTTATTGGTGGGCCTGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGGTAT

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|124986963|gb|EL059448.1|EL059448
EST:     GACATAAGACTTGAAAAATGGGGACTTCCTCCATTTCCAAGACT                         GGATAGAGAACACTTTACCAATTGATCCATGGCATATTGGAGGTCCAGTCA
genomic: GACATAAGACTTGAAAAATGGGGACTTCCTCCA-TTCCAAGACTgtaaaaattc ... gtatttgcagGGATAGAGAACACTTTACCAATTGATCCATGGCATATTGGAGGTCCAGTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacatgttcatctcggtaatgagacttttataccttgtaatttgtatttgcagGGATAGAGAACACTTTACCAATTGATCCATGGCATATTGGAGGTCCAGTCATCAAAGGATTTGGCCGTGGCTCTAAAGTACTCGGAATCCCCACCG
 tgataac  putative branch site (score: 2)
                                    ttgtaatttgtattt  TA-rich tract