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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattacatttccaacttcttagaattcccaacttaactctatctgaatctgatggctgcaagactattagattaccctcttaggagcctcctagttgttgcgcaccgcagattgcctgtattgcattttttaccatttttaccatgacaccgaagaaattaacctttttccctttgtttgaacattgcacagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGT

Basic information

species Arabidopsis thaliana
transcript AT2G38280.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g28180.2 (Oryza sativa), 3'ss of exon 5
gtaattacatttccaacttcttagaattcccaacttaactctatctgaatctgatggctgcaagactattagattaccctcttaggagcctcctagttgttgcgcaccgcagattgcctgtattgcattttttaccatttttaccatgacaccg--aagaaattaacctttttccctttgtttgaacattgcacagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGT
                                                                                             |   | ||| |  |    ||||   | |  |   ||| |      | | |  |||  |||   |   | || |   |     ||| ||||   | ||    || |||||| |||| || ||  |  | ||||| ||||| ||||||||||| |||||||||||||| || |||||||| ||||| || || ||||| ||||||
--------------------------------------------------------------------------------------------gtgtgttttgagagct-tggatt--ttatcctatgtttatactttatataatgatggaaccactatttagttgattatcaattcttcgtttt--ctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGT

upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G416667_T03 (Zea mays), 3'ss of exon 9
gtaattacatttccaacttcttagaattcccaacttaactctatctgaatctgatggctgcaagactattagattaccctcttaggagcctcctagttgttgcgcaccgcagattgcctgtattgcattttttaccatttttaccatgacaccgaagaaattaacctttttccctttgtttgaacattgcacagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGT
                                                                                        | |     || |  |    || | || |     | ||  ||   ||    |  ||| ||      |  || | ||  || ||  | | |  ||     || | ||| ||||| ||||| || ||  |  | ||||| |||||||||||||| || |||||||||||||| || ||||| ||||| || || || ||||| ||||||
---------------------------------------------------------------------------------------acatgtacattctcccctttcggatatagtaacaaatgagttgcctattcctaatac-ata----tgttgacacta--ctgttggcttataattcttattttctcagGTATGATCTGAATGTTGATTTGCTAGATGTCCATGCAGACAAAAGCACATTTCATCGTTTTGACAAATTCAATCTAAAATACAATCCATGTGGCCAAAGT

upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 8
gtaattacatttccaacttcttagaattcccaacttaactctatctgaatctgatggctgcaagactattagattaccctcttaggagcctcctagttgttgcgcaccgcagattgcctgtattgcattttttaccatttttaccatgacaccgaagaaattaacctttttccctttgtttgaacattgcacagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGT
                                                                                                  ||   |  |      |||    ||||  |||| | |     |  | |   |      || |||| | | | ||   |   ||| ||||       ||||||| || || || ||||||||||| ||||| |||||||| ||||| |||||||| |||||||||||||| || || || || |||||||||||||||
--------------------------------------------------------------------------------------------------gtaatgagctt----ttgtaattattatatttataattggct--agctgtatgtttcaggaattgatcctcttttgtcctttttaaca-------gATATGATCTCAATGTTGACCTTTTGGACGTTCACGCAGACAAGAGTACTTTTCATCGCTTTGATAAGTTCAATCTTAAATACAATCCTTGTGGTCAAAGT

upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 9
gtaattacatttccaacttcttagaattcccaacttaactctatctgaatctgatggctgcaagactattagattaccctcttaggagcctcctagttgttgcgcaccgcagattgcctgtattgcattttttaccatttttaccatgacaccgaagaaattaacctttttccctttgtttgaacattgcacagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGT
                                                                                                  ||   |  |      |||    ||||  | || | |     |  | |   |      || |||||| | | | |  |   |||  |      ||||||||||||| || || ||||||||||| ||||| |||||||| ||||| |||||||| |||||||||||||| || || || || ||||| |||||||||
--------------------------------------------------------------------------------------------------gtaatgagctt----ttgtaattattatagttataattggct--agctgtatgttttaggaattaatcctctgctgtcctttttta------acagATATGACCTCAATGTTGACCTTTTGGACGTTCACGCAGACAAGAGTACTTTTCATCGCTTTGATAAGTTCAATCTTAAATACAATCCTTGCGGTCAAAGT

upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 8
gtaattacatttccaacttcttagaattcccaacttaactctatctgaatctgatggctgcaagactattagattaccctcttaggagcct----cctagttgttgcgcaccgcagattgcctgtattgcatttttta-ccattt-ttaccatgacaccgaagaaattaacctttttc--cctttgtttgaacattgcacagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGT
                                                        |    || |  ||| | ||    | |||  |   |    || || ||| | |    |    |    | | || ||  |||||  |||||   |   ||| ||    |||  ||||||   |   | |||||||||||       || ||||||||||| || |||||||| ||||||||||||||||| || || ||||||||||||||||||||||| || ||||| || || || |||||||||
--------------------------------------------------------gtaataaaa--atttgtttttttttttaatactatttgaccaagatgt-gtgtgtggggagtgtaattttttacaccttttagtcatttaccattttgaaactct-gaatataacctcactgaacttttgtttgaac-------agGTATGACCTGAATGTTGACCTTTTAGATGTTCATGCAGACAAGAGCACATTTCATCGTTTTGATAAGTTCAATCTCAAGTACAATCCCTGCGGTCAAAGT

upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaattacatttccaacttcttagaattcccaacttaactctatctgaatctgatggctgcaagactattagattaccctcttaggagcctcctagttgttgcgcaccgcagattgcctgtattgcattttttaccatttttaccatgacaccgaagaa-attaacctttttccctttgtttgaacattgcacagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGT
                                                                              || |     | || ||| || ||            |||  |   ||  ||  | ||||| ||| |  ||||     | | | ||  ||| |  |    |||| |    |||||  || || ||||| || || ||| |  ||||||||||||| ||||||| ||| ||||||||||| || ||||||||||| || || || |||||||| || |||
-----------------------------------------------------------------------------gctttc----gtcttctaattattt-----------ttgtttcctttttatagtataccactttgaa-atgattttcatgtatatctaccgtgctggtcttgtgtctgaattgc--agTTACGACCTTAATGTGGACTTGCTGGATGTTCATGCTGACAAAAATACGTTTCATCGTTTCGACAAGTTCAACCTGAAATACAATCCTTGTGGCCAGAGT

upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaattacatttccaactt---cttagaattcccaacttaactctatctgaatctgatggctgcaagactattagattaccctcttaggagcctcctagttgttgcgcaccgcagattgcctgtattgcattttttaccatttttaccatgacaccgaagaaattaacctttttccctttgtttgaacattgca-cagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGT
||||  | ||     |  |   |||| |    |    || | | ||| |  || | ||    |  |  |  | |  ||   || |||  | |  |    |||      |    | ||| ||  ||| |   |||  |  ||    |  |    |    | ||  |     |  | | | | | ||  ||| | | ||| |||||  | || || ||| | |||||||||||||  |||||||  || || || |||||||||||||||||||| ||||| || || || || ||||| 
gtaagcagatccatgagattaacttaaaccatcatctttgaatatatatatatat-atataagataagcattgaccttgatctattacaaactacaggattg------aatataaatt-ccaatat-gtggtttgaagtatgcaaaatagataattatataatgtgg---tgatacatatatatgtgcatggtaacagTTATGATTTAAATGTAGACTTGTTGGATGTTCATGTTGACAAAAACACATTCCACCGTTTTGATAAGTTCAACCTTAAGTACAATCCATGCGGCCAAAGC

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|124775008|gb|EH865137.1|EH865137
EST:     GGAACATATTTGACCTTGAGAGAAGTTTTTGAGAGCCTGGATCTGACTGG                         ATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTT
genomic: GGAACATATTTGACCTTGAGAGAAGTTTTTGAGAGCCTGGATCTGACTGGgtaattacat ... cattgcacagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaccatgacaccgaagaaattaacctttttccctttgtttgaacattgcacagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGT
                   aattaac  putative branch site (score: 2)
                  aaattaaccttttt  TA-rich tract