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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttcttttttgctccagaccatcatgcaagaagactttgttagatattccaactacacatacttatctgtctgctccacactgatattatcggagaattgtacgtcttttcccattttcccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAGATCCCACGAATGTTTGATCCTTGGGGTGGCTACAGCATAATTGGATTTG

Basic information

species Arabidopsis thaliana
transcript AT1G01650.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g51430.1 (Oryza sativa), 3'ss of exon 10
gtaagtttttcttttttgctccagaccatcatgcaagaagactttgttagatattccaactacacatacttatctgtctgctccacactgatattatcgga-gaattgtacgtcttttcccattttcccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAGATCCCACGAATGTTTGATCCTTGGGGTGGCTACAGCATAATTGGATTTG
                                               ||  | ||      |   || ||   || |||| |      |||| | || |    |  |       || | |   | | |  |  | ||||||| ||||||||||  |  |  || |||||  | || ||| ||||||| || ||||||||||||||||| ||||| || |||||||| |||||||| |
----------------------------------------------gtaagttttgtggaaatttattctagact-tctggtaattggtgatctcattgtttaagctaagttggttatgctggtgtgcttctcaaagGTAGCTCGTGGTGACAAGACTGATGAAGACGGCGTCCCCATGTTACTAAAAATTCCACGAATGTTTGATCCATGGGGAGGATACAGCATCATTGGATTCG

upper sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 10
gtaagtttttcttttttgctccagaccatcatgcaagaagactttgttagatattccaactacacatacttatctgt-ctgctccacactgatattatcggagaattgtacgtcttttcccattttcccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAGATCCCACGAATGTTTGATCCTTGGGGTGGCTACAGCATAATTGGATTTG
                                           | | || | ||  | |||   ||||||    ||| ||||| |       |   |   | ||| ||    |  || |||      |  |   ||||| ||||||||||| |  |  |  || |||||  | || |||||  |||| |||||||||||||||||||| |||||||| | ||| || ||||| ||||
------------------------------------------gtaggtacagatgactacttt-catactgtgatgttctgcttc-------tgcaacttgcgaaatgc---taattgccctagcgtctgctcgtagGTTGCCCGTGGTGATAAGACTGATGAAGACGGTGTGCCCATGCTGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTG

upper sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
gtaagtttttcttttttgctccagaccatcatgcaagaagactttgttagatattccaactacacatacttatctgtctgctccacactgatattatcggagaattgtacgtcttttcccattttcccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAGATCCCACGAATGTTTGATCCTTGGGGTGGCTACAGCATAATTGGATTTG
                                             || ||    |  ||    |      ||| ||   |   |   ||||  ||  | |   || | | ||   || |     | |  || |||||| || ||||| ||||  | ||  ||||| ||  | || ||||| ||||| ||||| |||||||||||||| |||||||| |||||||| ||||| ||||
---------------------------------------------gtaagcgtgtgaaaggggattctgctatttggtggtatc---ctgaattttgctggttatagcatgttggtttc-----ttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG

upper sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 10
gtaagtttttcttttttgctccagaccatcatgcaagaagactttgttagatattccaactacacatacttatctgtctgctccacactgatattatcggagaattgtacgtcttttcccattttcccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAGATCCCACGAATGTTTGATCCTTGGGGTGGCTACAGCATAATTGGATTTG
|| |||  ||  ||        ||| |  | | | | || |          | ||     | | |||| |        || |  |  ||  | ||||   |  | || |    ||||| | | ||      |  ||||||| || ||||| || || ||||| || || || || |||||||| ||||| ||||| |||||||||||||||||||| |||||||| ||||| ||||
gtgagtgatttcttgga-----agatctcccttcgacaatatcacaaagcttgtttttgat-ctcataat-----acatgattgatgcttttcttattaaactaatgca-acattttcacttctt------tgcagGTAGCTCGAGGTGATAGGAGTGGAGAAGATGGTATCCCTATGCTACTCAAGATACCACGTATGTTTGATCCTTGGGGTGGTTACAGCATCATTGGTTTTG

upper sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G46760.1 (Glycine max), 3'ss of exon 10
gtaagtttttcttttttgctccagaccatcatgcaagaagactttgttaga-tattccaactacacatacttatctgtctgctc---cacactgatattatcggagaattg-tacgtcttttcccattttcccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAGATCCCACGAATGTTTGATCCTTGGGGTGGCTACAGCATAATTGGATTTG
                           ||   |    |   ||   ||||| |||||     | |  |  || | | |||  |    ||   || | || |     || |  | |  | ||| |  || |      |  ||||||| || ||||| || || ||||| || || || || |||||||| ||||| ||||| ||||||||||| |||||||| |||||||| ||||| ||||
--------------------gtgagtgatttcgaggaagatctcccttagactattcttcacaaagcttgttttttatctcataaaacatgatgcttttcttattaaactaatgcaacattttcacttctt-----tgcagGTAGCTCGAGGTGATAGGAGTGGAGAAGATGGTATCCCTATGCTACTCAAGATACCACGTATGTTTGATCCCTGGGGTGGTTACAGCATCATTGGTTTTG

upper sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtttttcttttttgctccagaccatcatgcaagaagactttgttagatattccaactacaca-tactt-atctgtctgctccacactgatattatcggagaattgtacgtcttttcccattttcccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAGATCCCACGAATGTTTGATCCTTGGGGTGGCTACAGCATAATTGGATTTG
||||||  ||        ||||| | | |  |     |  | |   || || |   |   |      ||||| |  | |||||| | || | | |  ||     ||||||     |||||             |||||||||| |||||||| || || || ||||| || ||||| |||||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||
gtaagtagttt-------ctccaaaacttgttagcccaccaatacatttgaaacggctgatgtttggtacttgagatctctgctgcccaattacagaattatgtaattgtg----ttttct-----------gtatagGTAGCTCGTGGTGATAGGAGTGGGGAGGATGGTATTCCGATGCTACTGAAGATCCCGCGAATGTTTGATCCTTGGGGTGGCTACAGCATCATTGGATTTG

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|124856943|gb|EH941380.1|EH941380
EST:     CGTGATGATTGTG                         GTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAG
genomic: CGTGATGATTGTGgtaagttttt ... ccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAG
EST: gi|124951493|gb|EL026856.1|EL026856
EST:     CCGTGAAAGCGTGATGATTGTG                         GTAGCCCGNGGNGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAG
genomic: CCGTGAAAGCGTGATGATTGTGgtaagttttt ... ccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacactgatattatcggagaattgtacgtcttttcccattttcccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAGATCCCACGAATGTTTGATCCTTGGGGTGGCTACAGCATAATTGGATTTG
    cactgat  putative branch site (score: 3)
                          tacgtcttttcccatt  putative PPT
       tgatattat  TA-rich tract