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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtgttgtccctactcattttcattctagaaatagtttttttcgctgctgctatctaaatatatcttttcactttgtgccaattgcagGTTCTTCGTCCTGGAGTTCTGTATTTCCTTCGTGATCCAGCAGATCCTAATTACAATCCATTCCGAGATTTGATTGATGATCCAGTGCACAAGCATGCTC

Basic information

species Arabidopsis thaliana
transcript AT4G34100.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34100.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G145104_T01 (Zea mays), 3'ss of exon 3
gtactgtgttgtccctactcattttcattc-tagaaatagttttt---ttcgctgctgctatctaaatatatcttttcactttgtgccaattgcagGTTCTTCGTCCTGGAGTTCTGTATTTCCTTCGTGATCCAGCAGATCCTAATTACAATCCATTCCGAGATTTGATTGATGATCCAGTGCACAAGCATGCTC
||| ||    |   ||    ||||  |     || | ||   |||   ||| |   ||     |  || |  ||||| || || |     | | ||||||| ||   ||||||||| ||||| || || || || || ||||| ||||||||||||||  | ||||||||||| ||||| ||||| |||||||| |
gtattgctcagctacttgatatttcgagcaacagcactaacatttaaattctcatatgtcccatccatcttactttttaccttatt---gtggtagGTTCTGCGCAATGGAGTTCTTTATTTTCTGCGGGACCCTGCTGATCCAAATTACAATCCATTTAGGGATTTGATTGACGATCCTGTGCATAAGCATGCCC

upper sequence: AT4G34100.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G051792_T01 (Zea mays), 3'ss of exon 3
gtactgtgttgtccctactcatttt------cattctagaaatagtttttttcgctgctg--ctatctaaat--atatcttttcactttgtgccaattgcagGTTCTTCGTCCTGGAGTTCTGTATTTCCTTCGTGATCCAGCAGATCCTAATTACAATCCATTCCGAGATTTGATTGATGATCCAGTGCACAAGCATGCTC
||| ||    | | ||    ||||       ||      ||| | ||   ||| ||  ||  || || |  |   | |||||| || || |     ||  |||| || ||   ||||||||| ||||| || || || || || ||||| ||||||||||||||  | |||||||||||||| || ||||| || ||||| |
gtattgctcagccacttgatatttcgagaaacagcactcaaacatttaaattcccttatgtcctgtccatctcactttcttttaaccttatt---gttatagGTGCTGCGCAATGGAGTTCTTTATTTTCTGCGGGACCCTGCTGATCCAAATTACAATCCATTTAGGGATTTGATTGATGACCCTGTGCATAAACATGCCC

upper sequence: AT4G34100.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S189_9V6.1 (Physcomitrella patens), 3'ss of exon 3
-gtactgtgttgtccctactcattttcattctagaaat--agtttttttcgctgct-gctatctaaatatatcttttcact----ttgtgcca-attgcagGTTCTTCGTCCTGGAGTTCTGTATTTCCTTCGTGATCCAGCAGATCCTAATTACAATCCATTCCGAGATTTGATTGATGATCCAGTGCACAAGCATGCTC
 ||||   |  |   | |    | |   | | |  ||   || |   |  | || | |  |  |   | |||   | || |    |||||     || |||||  |    || || ||| |||||||||| || ||||| || ||||| || ||||| |||||||| ||| |||| ||||||||  ||||||||||||| |
tgtacaa-gaaggaacaatgggtgtgggtccgaacaagggaggtgcgtgtggtgttagtcacgtgcgtttattgatccattgggattgtgttgcgttccagGTGTTGAAACCAGGGGTTTTGTATTTCCTGCGGGATCCGGCGGATCCAAACTACAACCCATTCCGGGATCTGATCGATGATCCCTTGCACAAGCATGCAC

upper sequence: AT4G34100.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ32433 (Selaginella moellendorffii), 3'ss of exon 4
gtactgtgttgtccctactcattttcattctagaaatagtttttttcgctgctgctatctaaatatatcttttcactttgtgccaattgcagGTTCTTCGTCCTGGAGTTCTGTATTTCCTTCGTGATCCAGCAGATCCTAATTACAATCCATTCCGAGATTTGATTGATGATCCAGTGCACAAGCATGCTC
                                  | | | | ||||  | |  | | ||||  |    ||  |   |||     | || |||||||| || ||||| || || |||||| | ||||| || || ||||| ||||||||||| ||||| || |||||||| |||||  | || ||||| ||| 
-------------------------------gtgagttgctattttttccgg-gttttctagttcatgctaatggtttta----agtttcagGTTCTCCGCCCTGGGGTCCTATATTTCTTGCGTGACCCGGCGGATCCAAATTACAATCCTTTCCGCGACTTGATTGACGATCCGCTTCATAAGCACGCTA

upper sequence: AT4G34100.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ20815 (Selaginella moellendorffii), 3'ss of exon 4
gtactgtgttgtccctactcattttcattctagaaatagtttttttcgctgctgctatctaaatatatcttttcactttgtgccaattgcagGTTCTTCGTCCTGGAGTTCTGTATTTCCTTCGTGATCCAGCAGATCCTAATTACAATCCATTCCGAGATTTGATTGATGATCCAGTGCACAAGCATGCTC
                                  | | | | ||||  | |  | | ||||  |    ||  |   |||     | || |||||||| || |||||||| || |||||| | ||||| || || ||||| ||||||||||| ||||| || |||||||| |||||  | || ||||| ||| 
-------------------------------gtgagttgctattttttccgg-gttttctagttcatgctaatggtttta----agtttcagGTTCTCCGCCCTGGAGTCCTATATTTCTTGCGTGACCCGGCGGATCCAAATTACAATCCTTTCCGCGACTTGATTGACGATCCGCTTCATAAGCACGCTA

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|125261746|gb|EL275831.1|EL275831
EST:     GAATCATGTACATGTTGCAAATAAGCATCTTCGTCAGCCTTCTTCGAGGG                         GTTCTTCGTCCTGGAGTTCTGTATTTCCTTCGTGAT
genomic: GAATCATGTACATGTTGCAAATAAGCATCTTCGTCAGCCTTCTTCGAGGGgtactgtgtt ... ccaattgcagGTTCTTCGTCCTGGAGTTCTGTATTTCCTTCGTGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttttcgctgctgctatctaaatatatcttttcactttgtgccaattgcagGTTCTTCGTCCTGGAGTTCTGTATTTCCTTCGTGATCCAGCAGATCCTAATTACAATCCATTCCGAGATTTGATTGATGATCCAGTGCACAAGCATGCTC
                   atctaaa  putative branch site (score: 3)
                  tatctaaatatatctt  TA-rich tract