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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctatcctctgaccacatcttcttatcccaagcatgtcttcttaattggtaaacatttgaacttttttattgtactgtgatgatcagTGTCGGAGACATATTTCCTCCAGTTAGCTTGAACTTTGCTGGTGGAGCATCTATGTTCTTGAATCCTCAGGATTACCTCATACAGCAGAACAATGTC

Basic information

species Arabidopsis thaliana
transcript AT5G22850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G05490.1 (Glycine max), 3'ss of exon 6
----------------------------------gtctatcctctgaccacatcttc-ttatcccaagcatgtcttcttaattggtaaacatttgaacttttttattgta-----------ctgtg--atgatcagTGTCGGAGACATATTTCCTCCAGTTAGCTTGAACTTTGCTGGTGGAGCATCTATGTTCTTGAATCCTCAGGATTACCTCATACAGCAGAACAATGTC
                                    || |  |   ||  |||| || || | | ||    ||  |   || | |   |  |    ||| | || || ||           ||||    || | ||||||   ||  | ||||||| ||| ||  |||||||||||||||| ||||||||| | || |  |||||||| ||||| |||||||||||     | 
gttaggctgaacatttaatgcctcctttttctgaacctttttttgcactccatcctccttttgctaattgagtgctaaaaaatagatcatctcgatactctctttttctaactccttttgtctgtactgtgtttagTGTCACTGAAGTTTTTCCTCAAGTAAGTCTGAACTTTGCTGGTGGTGCATCTATGATTTTAAGGCCTCAGGACTACCTGATACAGCAGAATTCCATT

upper sequence: AT5G22850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0061g01030.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------gtctatcct-ctgaccac--atcttcttatcccaagcatgtctt-----cttaattggtaaacatttgaacttttttattgtactgtgatgatcagTGTCGGAGACATATTTCCTCCAGTTAGCTTGAACTTTGCTGGTGGAGCATCTATGTTCTTGAATCCTCAGGATTACCTCATACAGCAGAACAATGTC
                                ||||    ||||| |  | |     ||    |  || | ||     || | ||  | |||||   || | | |   | | ||||     ||||||||   |  ||||||||| |||| || ||||||||||||||||| | |||||||    | || ||| |||| |||||  ||||||||||     | 
gtcctctttctagatttatgattttcagttcttatctggttgaccgctcagccctgcatagttattatcttttgcagactaattttcttaacatccaaaatgtatgtctattctgta---ttcagTGTCAAGGGTATATTTCCTACAGTCAGTTTGAACTTTGCTGGTGGTGTATCTATGAATCTAAAACCTGAGGACTACCTTCTACAGCAGAATTCCATT
















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|124809938|gb|EH895254.1|EH895254
EST:     AAAGGGAACCAATGTTACGTAATAACCACAAG                         TGTCGGAGACATATTTCCTCCAGTTAGCTTGAACTTTGCTGGTGGAGCATC
genomic: AAAGGGAACCAATGTTACGTAATAACCACAAGgtctatcctc ... tgatgatcagTGTCGGAGACATATTTCCTCCAGTTAGCTTGAACTTTGCTGGTGGAGCATC
EST: gi|164067146|gb|ES150865.1|ES150865
EST:     GTCAGACCCGTTGTTTCGAAAGGGAACCAATGTTACGTAATAACCACAAG                         TGTCGGAGACATATTTCCTCCAGTTAGCTTGAAC
genomic: GTCAGACCCGTTGTTTCGAAAGGGAACCAATGTTACGTAATAACCACAAGgtctatcctc ... tgatgatcagTGTCGGAGACATATTTCCTCCAGTTAGCTTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtcttcttaattggtaaacatttgaacttttttattgtactgtgatgatcagTGTCGGAGACATATTTCCTCCAGTTAGCTTGAACTTTGCTGGTGGAGCATCTATGTTCTTGAATCCTCAGGATTACCTCATACAGCAGAACAATGTC
       tcttaat  putative branch site (score: 3)
                 taaacatttgaacttt  TA-rich tract