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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacttgcctctcatttttaagataacccagagaaggagatttagaacttgttgaagttgaaactcttgattttaatttgttatacagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGCGACTAACATGCTTGAGAGTATGATAGTTCATCCAACTCCAACCCGGGCAG

Basic information

species Arabidopsis thaliana
transcript AT5G52920.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------------------------------------------------------gttagtact-tgcctctcatttttaagataacccagagaaggagattt------agaacttgttgaagttgaaac-----tcttga----ttttaatttgttatacagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGCGACTAACATGCTTGAGAGTATGATAGTTCATCCAACTCCAACCCGGGCAG
                                                                                     |||  | |  | | |   |  | ||  ||    |   |||  ||  ||       |||    || |  |  ||||     ||||      || |   |  | || ||||| || || ||||   ||||| | || ||||||||||||||||||||||| ||||| ||||| || |||||||| |||||||||||||||||||| ||||
gtatgatgcaatcgatcatattgctcgtactccattgtgctaacatgtccattacaacctgaggcttgaaaaagccattactttggttgtttccgtactttctagatctataatttgtccaggaaatagtcttcatgctggaatgcattaacatacaaacagcagtcttagaattttctgtgtcttcatgcagGAAGAAATTATTAGAATGTGCAGGAGCATGGGAAAAGCTGTTATTGTTGCCACTAATATGCTAGAAAGTATGATTGTTCATCCAACTCCAACCCGAGCAG

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 7
---gttagtacttgcctctcatttttaagataacccagagaaggagatttagaacttgttgaagttgaaact--cttg---attttaatttgttatacagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGCGACTAACATGCTTGAGAGTATGATAGTTCATCCAACTCCAACCCGGGCAG
   | |     |   || ||| |    | |||           |    | |     | |   | ||  | ||  ||||   ||| |  | | |  | ||||| || || ||||   ||||| | || ||||| || |||||||||||||| || || ||||| || |||||||| |||||||||||||||||||| ||||
agtgcttactataagctgtcagtaaagaaatattttttcctttgccgatgaaggtgtttcagatttacatcttccttgaatattatgttctttcctgcagGAAGAAATTATTAGAATGTGCAGGAGCATGGGGAAGGCTGTTATTGTTGCTACAAATATGCTCGAAAGTATGATTGTTCATCCAACTCCAACCCGAGCAG

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 7
-------------------------gttagtacttgcctctcatttttaagataacccagagaaggagatttagaacttgttgaagttgaaactcttgattttaat--ttgttat-acagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGCGACTAACATGCTTGAGAGTATGATAGTTCATCCAACTCCAACCCGGGCAG
                           |||||        |     ||   || |   |        |||  |   | ||||||  |   | ||    ||  ||||   ||||||   |||| ||||| || ||| |||| ||||| |||||||| ||||||||||| || || || ||||| || || ||||| ||||| |||||||||||| | ||||
gtaaacttctttacctctgaaaatctgtagtaaaaataattatcaattggtatcatttatgttgctggatggatgtcatgttgagctc--atcttaacatcgtaatggctgttattgtagGAAGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 7
---------------------------------gttagtacttgcctctcatttttaagataacccagagaaggagatttagaacttgttgaagttgaaactcttgattttaatttgttat-acagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGCGACTAACATGCTTGAGAGTATGATAGTTCATCCAACTCCAACCCGGGCAG
                                 | || |  |    |   ||  || |    ||    || | |  |||| || ||  |      | ||  || | ||      |||||||   |||| ||||| || ||  |||| ||||| |||||||| ||||||||||| || || || ||||| || || ||||| ||||| |||||||||||| | ||||
gtaaactcctttacctcttaaatccatagtaaagataattatcaattggtatcatttatgccactggaaggatgtcattttgagctcatc-----ttaacatcgtaat----gcttgttattgtagGAAGAGATAATCAATTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 7
gttagtacttgcctctcatttttaagataacccagagaaggagatttagaacttgttgaagtt--gaaactcttgattttaatttgttatacagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGCGACTAACATGCTTGAGAGTATGATAGTTCATCCAACTCCAACCCGGGCAG
|| |   | |      ||    | |||| |    |  || || | |||  | ||| |   | |  | |||     |   |  ||  | ||  |||| ||||| || | | | |||||||| |||||||| ||||||||||| || || || ||||| || || ||||| ||||| ||||| |||||| | || |
gtaaagtccttttaaacagaaatgagattaat--ggtaaagataattatcagttggtattgcttcgtaacataaaaaaatgcttgctaatgtagGAAGAGATAATAAGCATATGCCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTGGAAAGCATGATTGTTCACCCAACACCAACCAGAGCCG

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 7
gttagtactt-gcctctcatttttaagataacccagagaaggagattt------agaacttgttgaagttga----aactcttgatttta--atttgtta-----------tacagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGCGACTAACATGCTTGAGAGTATGATAGTTCATCCAACTCCAACCCGGGCAG
|| | | ||| |  ||| |||    |||| |   ||| ||   | | |      ||  | | |     || |    ||   |  | || |  ||||   |           | ||||| ||||| || |   | || ||||| |||||||||||||||||||| || || || ||||| || || ||||| ||||| ||||| |||||||| ||||
gtaatttctttgtttctgattgaagagatgatagagataatagggtcttccagaagtgcctttcatgttttataacaagcatctacttgagtatttaccaacatttcaaactgcagGAAGAGATAATCAGGATATGTCGTAGCATGGGAAAAGCTGTTATTGTAGCAACCAATATGCTGGAAAGCATGATTGTTCACCCAACACCAACCCGAGCAG

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|124952603|gb|EL027860.1|EL027860
EST:     GAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG                         GAGGAGATCATTAACCTGTGCCGTAGTAT
genomic: GAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAGgttagtactt ... tgttatacagGAGGAGATCATTAACCTGTGCCGTAGTAT
EST: gi|124705603|gb|EH797005.1|EH797005
EST:     GAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG                         GAGGAGATCATTAACCTGTGCCGTAGTATGGGAA
genomic: GAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAGgttagtactt ... tgttatacagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAA
EST: gi|125292188|gb|EL306273.1|EL306273
EST:     AGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG                         GAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGC
genomic: AGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAGgttagtactt ... tgttatacagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggagatttagaacttgttgaagttgaaactcttgattttaatttgttatacagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGCGACTAACATGCTTGAGAGTATGATAGTTCATCCAACTCCAACCCGGGCAG
                                     ttttaat  putative branch site (score: 3)
                               tcttgattttaatttg  TA-rich tract