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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgattcgatccttgcaatactaaaaaccaatcaaagaaaggtgtttttttgtttgtttgttactaatgcaaataaatctatcatacgtagTCTGCTATTCTTGGAATGCATTCAATTGTGCAACGTCCAATGGTTGTGGGAGGAAGCGTAGTTCCGAGGCCAATGATGTATGTCGCGCTGACTTACGATC

Basic information

species Arabidopsis thaliana
transcript AT5G55070.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55070.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 12
gttcgattcgatccttgcaatactaaaaaccaatcaaagaaaggtgtttttttgtttgtttgttactaatgcaaataaatctatcatacgtagTCTGCTATTCTTGGAATGCATTCAATTGTGCAACGTCCAATGGTTGTGGGAGGAAGCGTAGTTCCGAGGCCAATGATGTATGTCGCGCTGACTTACGATC
|| |  ||  ||  |||| |     ||||     |      ||||   | ||  ||  | ||  || |||| | ||| |||||    | | |||||||||||||||||||||| || ||||| ||||| ||  |||| ||||  || | | |  |  ||||||||||||||||  | |||||||| || || |
gtcctttttcatttttgccacttgcaaaaattgccctcactaggttgatattcattcatctgacac-aatgtatatatatcta----atgcagTCTGCTATTCTTGGAATGCACTCCATTGTACAACGCCCTGTGGTCGTGGACGGCAACATTCTCGCGAGGCCAATGATGTACCTTGCGCTGACATATGACC

upper sequence: AT5G55070.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ31629 (Selaginella moellendorffii), 3'ss of exon 8
gttcgattcgatccttgcaatactaaaaacca-atcaaagaaaggtgtttttttgtttgtttgttactaatgcaaataaatctatcatacgtagTCTGCTATTCTTGGAATGCATTCAATTGTGCAACGTCCAATGGTTGTGGGAGGAAGCGTAGTTCCGAGGCCAATGATGTATGTCGCGCTGACTTACGATC
                    |    |    || |||  ||||     | ||||  ||   || ||  |            | | |  | |  ||||||||||||||||||||||||| ||   | | |||||  ||||  | ||        ||||     | || ||||||||  | ||  |||| |||||||
-------------------gtttggaccttcacatctcagaagaccttgttttcattgaatttttgtt------------tttgttttcc--agTCTGCTATTCTTGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGCAACGAAATAGTCATCCGACCGATGATGTACATTGCTTTGACATACGATC
















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|164134318|gb|ES189988.1|ES189988
EST:     TCAACCCTCCTCAG                         TCTGCTATTCTTGGAATGCATTCAATTGTGCAACGTCCAATGGTTGTGGGA
genomic: TCAACCCTCCTCAGgttcgattcg ... tcatacgtagTCTGCTATTCTTGGAATGCATTCAATTGTGCAACGTCCAATGGTTGTGGGA
EST: gi|164081054|gb|ES036657.1|ES036657
EST:     TCAACCCTCCTCAG                         TCTGCTATTCTTGGAATGCATTCAATTGTGCAACGTCCAATGGTTGTGGGA
genomic: TCAACCCTCCTCAGgttcgattcg ... tcatacgtagTCTGCTATTCTTGGAATGCATTCAATTGTGCAACGTCCAATGGTTGTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaggtgtttttttgtttgtttgttactaatgcaaataaatctatcatacgtagTCTGCTATTCTTGGAATGCATTCAATTGTGCAACGTCCAATGGTTGTGGGAGGAAGCGTAGTTCCGAGGCCAATGATGTATGTCGCGCTGACTTACGATC
                         tactaat  putative branch site (score: 1)
                                  aaataaatctatcata  TA-rich tract