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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatacaaacggtttctttcccaaaatagattttattttattattattagtatcttaataatcatatttttattgttattgatcgtgcatgattatgtttcagCTACATCACACAGACAAGTTCAATGGTGTACCATATGGACTGTTTCTTGGACCCAAG

Basic information

species Arabidopsis thaliana
transcript AT4G25700.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G25700.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g48880.1 (Oryza sativa), 3'ss of exon 4
---------------gtaaatacaaacggtttctttcccaaaatag--attttattttattattattagtatc--ttaataatcatatttttattgttattgatcgtgcatgattatgtttcagCTACATCACACAGACAAGTTCAATGGTGTACCATATGGACTGTTTCTTGGACCCAAG
                |    ||  ||| || ||   |||  |     | |  |   |  || || || ||     ||   |   || ||||  || | ||  | |||  ||   | |   ||| |||| ||||| ||||||||| | || ||||| ||||| ||||||||||||||||||
gtacgagaccaccagctgctcactgacgtttactgcaccactactactagtccacgctgctactactactactggctagagagtgtacttttgctgattttctttgtg--tggccacgag-cagATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGACCCAAG
















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|86061534|gb|DR357291.1|DR357291
EST:     GTCCCATCGCCGACGTCCCTTACCTCCGAAAGGTCGCCGCCGCTCACCAG                         CTACATCACACAGACAAGTTCAATGGTGTA
genomic: GTCCCATCGCCGACGTCCCTTACCTCCGAAAGGTCGCCGCCGCTCACCAGgtaaatacaa ... tatgtttcagCTACATCACACAGACAAGTTCAATGGTGTA
EST: gi|47830828|gb|CK120512.1|CK120512
EST:     GTCCCATCGCCGACGTCCCTTACCTCCGAAAGGTCGCCGCCGCTCACCAG                         CTACATCACACAGACAAGTTCAATGGTGTACCATATGGACTGTTTCTTGGA
genomic: GTCCCATCGCCGACGTCCCTTACCTCCGAAAGGTCGCCGCCGCTCACCAGgtaaatacaa ... tatgtttcagCTACATCACACAGACAAGTTCAATGGTGTACCATATGGACTGTTTCTTGGA
EST: gi|124838031|gb|EH922470.1|EH922470
EST:     GTCCCATCGCCGACGTCCCTTACCTCCGAAAGGTCGCCGCCGCTCACCAG                         CTACATCACACAGA
genomic: GTCCCATCGCCGACGTCCCTTACCTCCGAAAGGTCGCCGCCGCTCACCAGgtaaatacaa ... tatgtttcagCTACATCACACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatcttaataatcatatttttattgttattgatcgtgcatgattatgtttcagCTACATCACACAGACAAGTTCAATGGTGTACCATATGGACTGTTTCTTGGACCCAAG
                            tattgat  putative branch site (score: 3)
      ttaataatcatatttt  TA-rich tract