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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgattcctagaccgacttcttcaatttctttgcattgttgtcaaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA

Basic information

species Arabidopsis thaliana
transcript AT1G50480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 4
gtgattgattcctagaccgacttcttcaatttctttgcattgttgtcaaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA------------
            |  ||   ||     |||  | ||  |  | |  ||    | || |     | |   ||||        |||   |   |    | ||||| ||||| |||||||| ||||| ||  | ||||||||||| || || || ||||||||| ||||||| |||||||| || || |||| | |||| | ||            
-----------atgaacatgctgtgggaatggcattagacagata-cactgaacacataacattctgctttattctgctgactg-actgacttccgtgcaggcggagaagcagATTGAAATGTATACCAAGCAAGGCTTCTCAAACCTCCCAATATGCATGGCGAAAACTCAGTACTCGTTTTCGCATGTTCCATCCATGAAGGGCGCGCCGT

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g27420.1 (Oryza sativa), 3'ss of exon 4
gtgattgattcctagaccgacttcttcaatttctttgcattgttgtcaaaagaaac-ctgtttatgtaac-ttatctattatcctg-tgatatgtaaa-----atacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA
        ||   | || ||  |   ||   | |  | || |   |  | ||| || |||   |  |||| || |   |||| ||| |||       |      | ||||| ||||| |||||||| ||||| ||  | ||||||||||| || || || ||||||||| ||||||| |||||||| || || |||| | |||| | ||
-------cttttgacactga--tgaacatgctgtgggaatggcattagacagatacactgaacacataacattctgctttattctgctgactgactgacttccgtgcagGCGGAGAAGCAGATTGAAATGTATACCAAGCAAGGCTTCTCAAACCTCCCAATATGCATGGCGAAAACTCAGTACTCGTTTTCGCATGTTCCATCCATGA

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G824944_T02 (Zea mays), 3'ss of exon 4
gtgattgattcctagaccgacttcttcaatttctttgcattgttgtcaaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA
||   |  ||  ||  |   |    |   ||  | |   | ||  ||| |   |  ||| | |  |  |||  |      |     |           ||||| ||||| |||||||||||||||||  | ||||| ||||| |  || ||||| |||||| |||| || |||||||| ||||||||||   | || | ||
gtatcttgttg-taaccatgccgtgtgtgttggtctttttggtcctcatac--actctgctgacttctcttgaccgacccctcccaa-----------cagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 4
-gtgattgattcctagaccgacttcttcaatttctttgcattgttgtcaaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA---
  |  ||| |  | |  |||  |   |   | | ||||    ||  ||| |   |  ||| | |  |  |||  |      |     |           ||||| ||||| |||||||||||||||||  | ||||| ||||| |  || ||||| |||||| |||| || |||||||| ||||||||||   | || | ||   
tcttgttg-taaccatgccgtgtgtgttggtctttttg----gtcctcatac--actctgctgacttctcttgaccgacccctcccaa-----------caggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 4
gtgattgattcctagaccgacttcttcaatttc---tttgcattgttgtcaaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA
   |||  || | |   |   ||     || ||   |||| | |  ||   ||     |    |  ||  | ||  |    || || |  | |||   | | |||| ||||||||||||||||||||||    |||||| || || ||||| ||||| |||||| | || || ||||||||||| |||||    || ||   ||
-ccattttttgcaatctcagtttgccagatgtcaaatttgaact--tgctgaacagttcagaatgttgccatttgacatgaattctctcttttgtgtga-atagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCCATCTGCATGGCCAAGACCCAGTACTCATTTTCACACACCGCTTCTGTGA

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ27738 (Selaginella moellendorffii), 3'ss of exon 4
gtgattgattcctagaccgacttcttcaatttctttgcattgttgtcaaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA
                           ||  |||     |  || || |       ||  ||      || || |  |   |   |||  ||     |||||||||   | |||| ||| | |||||   ||||||||||||| | |||||||| |||||| |||| || |||||||| ||||| || ||| ||||    |
-------------------------gtaagctctccatttgcttctcga------tcttctt------ctcatttgctcgtcc-cgat-cgttgctcacagGCAGAAGCAAAGATCGAGCTCTACACGAGACAAGGCTTCTCGCAACTTCCCATTTGCATGGCGAAGACGCAGTACTCGTTCTCGCACGATCCATCGCTCA

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ37206 (Selaginella moellendorffii), 3'ss of exon 5
gtgattgattcctagaccgacttcttcaatttctttgcattgttgtcaaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA
                                    | |   |   ||   |   |  | || | |  || || |  |   ||  |||  ||     |||||||||   | |||| ||| | ||||| | ||||||||||||| | |||||||| |||||| |||| || |||||||| ||||| || ||| ||||    |
------------------------------------gtaagctctccatttgcttctcgattttctt-ctcatttgctcgtct-cgat-cgtcgctcacagGCAGAAGCAAAGATCGAGCTCTACACGCGACAAGGCTTCTCGCAACTTCCCATTTGCATGGCGAAGACGCAGTACTCGTTCTCGCACGATCCATCGCTCA

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|163986805|gb|ES111815.1|ES111815
EST:     AGGCAATAGCTAAGTCATATGGAGCCAGTGGTGTTGAATATTCAGACCAG                         GCAGAGAAACAGATTGAGATGTACACACAACAAGGCTT
genomic: AGGCAATAGCTAAGTCATATGGAGCCAGTGGTGTTGAATATTCAGACCAGgtgattgatt ... taaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA
                atgtaac  putative branch site (score: 3)
             tttatgtaacttatct  TA-rich tract