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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattatactccctgattcggtttgatcacgttaaaatatcgtttaccggtttaatgattttgtgtttggtgtgtatgtgaatcagATCTTGGAAAAGTTCTTCTTCACTCTTCATTTGGTGAGCTCCCTCAGTGGGCTGTCGTCGGTGATACATTTCCAGTGGGATGTGCTTTTGATGAATCTAT

Basic information

species Arabidopsis thaliana
transcript AT1G14520.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G126900_T03 (Zea mays), 3'ss of exon 3
--gtaaattatactccctgattcggtttgatcacgttaaaatatcgtttaccggtttaatgattttgtgtttggtgtgtatgtgaat--cagATCTTGGAAAAGTTCTTCTTCACTCTTCATTTGGTGAGCTCCCTCAGTGGGCTGTCGTCGGTGATACATTTCCAGTGGGATGTGCTTTTGATG-AATCTAT------
   |    |  ||| | || ||  | ||| | || |    ||  |   |  ||     | | || | |  |     |   ||| | |  |||| || || || || || || ||| |    || || ||||||||||||||||||||||||||| |        ||  ||||  |  |   |||| ||| ||       
gtatggcctgcactgcttgctt--gcttgcttac-tgccgatg-caactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGGTAAG-------CAAGGGGAAATCTTGGCGATGCAATATAATACTCA

upper sequence: AT1G14520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G126900_T01 (Zea mays), 3'ss of exon 2
--gtaaattatactccctgattcggtttgatcacgttaaaatatcgtttaccggtttaatgattttgtgtttggtgtgtatgtgaat--cagATCTTGGAAAAGTTCTTCTTCACTCTTCATTTGGTGAGCTCCCTCAGTGGGCTGTCGTCGGTGATACATTTCCAGTGGGATGTGCTTTTGATGAATCTAT
   |    |  ||| | || ||  | ||| | || |    ||  |   |  ||     | | || | |  |     |   ||| | |  |||| || || || || || || ||| |    || || |||||||||||||||||||||||||                                        
gtatggcctgcactgcttgctt--gcttgcttac-tgccgatg-caactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG----------------------------------------
















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|19878336|gb|AU239167.1|AU239167
EST:     AAAAGATTACCCTGATGAAGACTGGCTCCATCTGACCGGTCTTATCCACG                         ATCTTGGAAAAGTTCTTCTTCACTCTTCATTTGGTGAGCTCCCTCAGTGGG
genomic: AAAAGATTACCCTGATGAAGACTGGCTCCATCTGACCGGTCTTATCCACGgtaaattata ... tgtgaatcagATCTTGGAAAAGTTCTTCTTCACTCTTCATTTGGTGAGCTCCCTCAGTGGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaatatcgtttaccggtttaatgattttgtgtttggtgtgtatgtgaatcagATCTTGGAAAAGTTCTTCTTCACTCTTCATTTGGTGAGCTCCCTCAGTGGGCTGTCGTCGGTGATACATTTCCAGTGGGATGTGCTTTTGATGAATCTAT
                  gtttaat  putative branch site (score: 4)
                   tttaatgattttgt  TA-rich tract