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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaaatcaaaataaccccgctccgattatgtgtatgtatgtattatcaagtagcctaaagcagagaagctcttgtccaatgttgtagTTCATGGAGTGGGTTGGTGAAGATACGAAGTGTCCGTACTGTGAAGGTCTTGGCTATACAGTTTGCGATGTCTGCGACGGCAAAAAAAACTTATAATAAT

Basic information

species Arabidopsis thaliana
transcript AT4G13670.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g43420.1 (Oryza sativa), 3'ss of exon 5
gtgagt--aaaatcaaaat--aaccccgctccgattatgtgtatgtatgtattatcaagtagcctaaagcagagaagctcttgtcca------atgttgtagTTCATGGAGTGGGTTGGTGAAGATACGAAGTGTCCGTACTGTGAAGGTCTTGGCTATACAGTTTGCGATGTCTGCGACGGCAAAA-AAAACTTATAATAAT
|| ||    |  || |  |  |    |||  |   || ||| || || ||||    |  ||  ||     |   |   |  |||  |      |   || ||||  |||||||||| |||||||||||||||||||| ||||||||||| ||||| |  |  || || ||||| || || || || | |  |   |  | | |
gtaagctcgagttccagttgcaggatcgcatcatata-gtgaatataagtat-gctatttattctctgatatgcacctttctgtttacccctcaaaatgcagTTTTTGGAGTGGGTCGGTGAAGATACGAAGTGTCCATACTGTGAAGGCCTTGGTTCAATTGTATGTGATGTTTGTGAAGGGAAGACAGTAGCCACGA-ACT

upper sequence: AT4G13670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G031721_T03 (Zea mays), 3'ss of exon 6
--------------------gtgagtaaaatcaaaataaccccgctccgattat-gtgtatgtatgtattatcaagtagcctaaagcagagaagctcttgtccaatgttgtagTTCATGGAGTGGGTTGGTGAAGATACGAAGTGTCCGTACTGTGAAGGTCTTGGCTATACAGTTTGCGATGTCTGCGACGGCAAAAAAAACTTATAATAAT--
                     ||   |||||  |   | |  | || |  |||  ||  |  | ||   ||||   | | || | |||      |  ||  |      || ||||| |||||||||| ||||||||||||||||| || |||||||||||  |||| |  |   | || ||||| || || ||  ||| ||| | ||   ||   
gtaaccaccgtagcctcctgttgcacaaaatgcatgcatcatcccttcagttaaagttaaattttgctctatcttcttgtctgacgcatt----ccttttcctcgaaatgcagTTCTTGGAGTGGGTCGGTGAAGATACGAAGTGCCCATACTGTGAAGGAATTGGTTCCATTTTGTGTGATGTTTGTGATGG--AAAGAAAGTAATGGCAAGTT
















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|125241209|gb|EL255294.1|EL255294
EST:     GTGAGCCAAACATTGAGCCGCAG                         TTCATGGAGTGGGTTGGTGAAGATACGAAGTGTCCGTACTGTGAAGGTCTT
genomic: GTGAGCCAAACATTGAGCCGCAGgtgagtaaaa ... aatgttgtagTTCATGGAGTGGGTTGGTGAAGATACGAAGTGTCCGTACTGTGAAGGTCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtatgtattatcaagtagcctaaagcagagaagctcttgtccaatgttgtagTTCATGGAGTGGGTTGGTGAAGATACGAAGTGTCCGTACTGTGAAGGTCTTGGCTATACAGTTTGCGATGTCTGCGACGGCAAAAAAAACTTATAATAAT
                    gcctaaa  putative branch site (score: 3)
     atgtattat  TA-rich tract