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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactccattacaaaagatctttcacattttgaattaaaattatgcattaatgccattaggatcaaaagacatgacctttctattttttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCTTCCCTTTTGTGCAATAGCTTATGCTCTTACCGGAATCTTCGGATCGTTA

Basic information

species Arabidopsis thaliana
transcript AT1G32080.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g32830.1 (Oryza sativa), 3'ss of exon 4
gtgactccattacaaaagatctttcacatt---ttgaattaaaattatgcattaatgc-cattaggat-caaaagacatgacctttctattttttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCTTCCCTTTTGTGCAATAGCTTATGCTCTTACCGGAATCTTCGGATCGTTA
 | ||     | |        |||   | |   || |  |  |  |||  |   |    ||  || || |   |   || |  |||  ||||    ||  ||||||||||||||| |||||||||||  ||||||| |||||||| || || || ||||| || || || ||||| |  || || || |||||||| ||| | 
-ttacctacctgctggctgctttttttagtaagttaagctgcatatatatacatacatacagcagtatgctctatgaataatgtttgcatttacgttg--cagTGCTCATGGACTGGGAACAGCAGCGCTGTCGGCCAAGGAGCCTGAAGCGCTGCCCTTCTGCGCCATCGCTTACGGCCTGACGGGGATCTTCGGTTCGCTC

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G15800.1 (Glycine max), 3'ss of exon 7
--gtgactccattacaaaagatctttcacattttgaattaaaattatgcattaatgccattaggatcaaaagacatgacctttctattttttatgga-cagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCTTCCCTTTTGTGCAATAGCTTATGCTCTTACCGGAATCTTCGGATCGTTA
   | | || ||  ||||    |  | | | || |||| | | ||      |     |||    ||  |   ||         |||  ||||||    |||||| || || |||||||||||||||||||| || ||||| || |||||||| || |||||||| || ||||||||||| |  || || || |||||  | 
aaattaatctataccaaacatgcaataatagtt-gaatgacattttctttgtgcgtgcatggttatttacttactctcttgacctaaattttatttttcagTGCCCACGGGCTTGGAACAGCAGCTTTGTCTGCCAAGGAACCCGAGGCTCTCCCATTTTGTGCCATTGCTTATGCTCTGAATGGTATATTTGGATCCATT

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G34440.1 (Glycine max), 3'ss of exon 6
-gtgactccattacaaaagatctttcacattttgaattaaaattatgcattaatg--ccattaggatcaaaagacatgacctttctattttttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCTTCCCTTTTGTGCAATAGCTTATGCTCTTACCGGAATCTTCGGATCGTTA
 |  |    |||  |  | |  |  ||       |  |||| |  |   ||  ||   |||        |         ||| |    |   | |  |||||  ||| || |||||||||||||| || || || ||||| || ||||||||||| |||||||| || ||||||||||| || ||||| || |||||  ||
agaaatggtatt-taggaaacatgccattaaggtagataaactattttcttgctgaggcatatatgcttatttttgcttcctcttggatgaatttatacagTTGTCACGGGCTTGGAACAGCAGCCTTATCTGCCAAGGAACCTGAGGCTCTTCCATTTTGTGCTATTGCTTATGCTCTGACTGGAATATTTGGATCTATA

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G34720.1 (Glycine max), 3'ss of exon 9
gtgactccattacaaaagatctttcacattttgaattaaaatt--atgcattaat--gccattaggatcaaaagacatgacctttctattttttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCTTCCCTTTTGTGCAATAGCTTATGCTCTTACCGGAATCTTCGGATCGTTA--
  || |   | | |||| |    | |  || | ||  || ||   | |||| |||  |  ||||    |  |     |   ||   ||||| || |  ||||||| ||  | |||||||||||||||||||| || ||||| || |||||||| || |||||||| || || |||||||| |  || || |  |||||  ||  
--gaatttttgaaaaaaaagtgattattttctcaacaaatatacaaagcatgaataagtgattatttacttactctttcgactaaatatttatttttcacagTGCCCACAGGCTTGGAACAGCAGCTTTGTCTGCCAAGGAACCTGAGGCTCTCCCATTTTGTGCCATTGCATATGCTCTGAATGGTATTT--GGATCTATACT

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G01340.1 (Glycine max), 3'ss of exon 6
-gtgactccat-tacaaaagatctttcacattttgaattaaaattatgcattaatgccattaggatcaaaagacatgacctttctattttttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCTTCCCTTTTGTGCAATAGCTTATGCTCTTACCGGAATCTTCGGATCGTTA
 |  |    || ||  ||| || |     |  | ||   |  ||| |    |     |||        |         ||| |    |   | |  |||||   || || || |||||||||||||| || || ||||| || ||||||||||| |||||||| || ||||||| ||| || || || || |||||  ||
agaaatagtatgtaggaaacatgtcattaaggtagataaactattttcttcttgaagcatatatgcttatttttgcttcctcttggatcaatttatacagTTGCCACGGGCTCGGAACAGCAGCTTTATCTGCCAAGGAACCTGAGGCTCTTCCATTTTGTGCCATTGCTTATGGTCTGACTGGGATATTTGGATCTATA

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv08s0056g01690.t01 (Vitis vinifera), 3'ss of exon 7
-gtgactccattacaaaagatctttcac-attttgaattaaaattatgcattaatgccattaggatcaaaagacatgacctttctattttttatgg--acagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCTTCCCTTTTGTGCAATAGCTTATGCTCTTACCGGAATCTTCGGATCGTTA
 |  |  | | ||       ||| | |  ||| | |  ||  ||   ||||   ||  || || |  | | |   |    | | | || |||   |  |||||||||||||||| || || || ||  |||| || ||||| || |||||||| || |||||||| || ||||||||||| || ||||| ||||| ||  | 
cgaaatacaagtatctggagtctattattattataagatatgat-gcgcat-gttgggatgagtaaaatatgttgtttgttgtttgttgtttgatgttacagTGCTCATGGACTGGGCACTGCGGCACTGTCAGCAAAGGAACCGGAGGCTCTCCCATTTTGTGCCATTGCTTATGCTCTCACTGGAATTTTCGGCTCACTC

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|125026871|gb|EL099140.1|EL099140
EST:     GGGGAATTGCAACTGCTTCAAG                         TGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCT
genomic: GGGGAATTGCAACTGCTTCAAGgtgactccat ... ttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCT
EST: gi|86080362|gb|DR376119.1|DR376119
EST:     AAACTGCGTTTACGTGATCCAATTGCTCGGGGAATTGCAACTGCTTCAAG                         TGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCT
genomic: AAACTGCGTTTACGTGATCCAATTGCTCGGGGAATTGCAACTGCTTCAAGgtgactccat ... ttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCT
EST: gi|47830990|gb|CK120674.1|CK120674
EST:     AAACTGCGTTTACGTGATCCAATTGCTCGGGGAATTGCAACTGCTTCAAG                         TGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCT
genomic: AAACTGCGTTTACGTGATCCAATTGCTCGGGGAATTGCAACTGCTTCAAGgtgactccat ... ttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCT
EST: gi|86080193|gb|DR375950.1|DR375950
EST:     AAACTGCGTTTACGTGATCCAATTGCTCGGGGAATTGCAACTGCTTCAAG                         TGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCT
genomic: AAACTGCGTTTACGTGATCCAATTGCTCGGGGAATTGCAACTGCTTCAAGgtgactccat ... ttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCT
EST: gi|125040682|gb|EL112951.1|EL112951
EST:     AAACTGCGTTTACGTGATCCAATTGCTCGGGGAATTGCAACTGCTTCAAG                         TGCTCATGGACTTGGAACAGCAG
genomic: AAACTGCGTTTACGTGATCCAATTGCTCGGGGAATTGCAACTGCTTCAAGgtgactccat ... ttatggacagTGCTCATGGACTTGGAACAGCAG
EST: gi|125109496|gb|EL161922.1|EL161922
EST:     AAACTGCGTTTACGTGATCCAATTGCTCGGGGAATTGCAACTGCTTCAAG                         TGCTCATGGACTTGGAACAG
genomic: AAACTGCGTTTACGTGATCCAATTGCTCGGGGAATTGCAACTGCTTCAAGgtgactccat ... ttatggacagTGCTCATGGACTTGGAACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcattaatgccattaggatcaaaagacatgacctttctattttttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCTTCCCTTTTGTGCAATAGCTTATGCTCTTACCGGAATCTTCGGATCGTTA
   cattaat  putative branch site (score: 3)
                                 cctttctattttttat  putative PPT
                                   tttctattttttat  TA-rich tract