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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGATTTGCTAAGCTACTTCTCGGGGAAGACATGTCTGGTGGAGGTAAAGGGGTTTGTACGGCGCTTGCTATCTCCAACGCCATCACCAATCTCTCTGgtaccatctcaatcttcttccctttttgttagttggtatatatagtaggggtttctagttttttaataaggctagtgtccacacag

Basic information

species Arabidopsis thaliana
transcript AT4G38430.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38430.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os09g37270.2 (Oryza sativa), 5'ss of exon 1
GAGAGATTTGCTAAGCTACTTCTCGGGGAAGACATGTCTGGTGGAGGTAAAGGGGTTTGTACGGCGCTTGCTATCTCCAACGCCATCACCAATCTCTCTGgtaccatctcaatcttcttccctttttgttagttggtatatatagtaggggtttctagtttt-ttaataaggctagtgtccacacag---------
||| | || || ||||| || ||||| || |||||||| ||  | || || || || || || ||||| || |||||||||||||||||||| ||||| |||||  ||   | |  |  |  ||   || | |||  |     || || |||   || | ||  |  |   | |  |||     | |         
GAGCGCTTCGCCAAGCTGCTGCTCGGCGAGGACATGTCCGGGAGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGCCATCACCAACCTCTCCGgtacggtcatgaacccccaca-ttgccgtgatttgcgacgaggag-agtggtgaataatgttgctgctgctgttgttgttgtttccgaatccgcag

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G105253_T01 (Zea mays), 5'ss of exon 2
GAGAGATTTGCTAAGCTACTTCTCGGGGAAGACATGTCTGGTGGAGGTAAAGGGGTTTGTACGGCGCTTGCTATCTCCAACGCCATCACCAATCTCTCTGgtaccatctcaatcttcttccctttttgttagttggtatatatagtaggggtttctagttttttaataaggctagtgtccacacag
||| | || || || || || ||||| || |||||||| ||  | || || || || || || ||||| || |||||||||||||||||||| ||||| |||||   ||| | |  |         || || |        || |   || |||||  |  |||     | | ||           
GAGCGCTTCGCCAAACTCCTGCTCGGCGAGGACATGTCCGGCAGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGCCATCACCAACCTCTCCGgtacg--ctcgagccgccg-------tgctactccacccgcattgcccggatttctgatggtttccct-gtccag-----------

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA12G02620.1 (Glycine max), 5'ss of exon 2
GAGAGATTTGCTAAGCTACTTCTCGGGGAAGACATGTCTGGTGGAGGTAAAGGGGTTTGTACGGCGCTTGCTATCTCCAACGCCATCACCAATCTCTCTGgtaccatctcaatcttcttccctttttgttagttggtatatatagtaggggtttctagtt---ttttaataaggctagtgtccacacag----------------
||||| ||||||||||| ||||| || || ||||||||||| || || |||||||| ||||| || ||||| |||||||| || || || ||||||||||||    |    |   ||||   |  |  |||  |  | ||  | | |     || ||| |   ||| |  |   | | |    | |||                 
GAGAGGTTTGCTAAGCTGCTTCTGGGAGAGGACATGTCTGGAGGCGGAAAAGGGGTGTGTACTGCACTTGCAATCTCCAATGCAATAACTAATCTCTCTGgt----tagtgactctcttatgtgctaattaagtaat-tagtttgcacaacgttgtagatacatttgaccataaccacttgtaaaacaacaataataagatgtta

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G10330.1 (Glycine max), 5'ss of exon 2
GAGAGATTTGCTAAGCTACTTCTCGGGGAAGACATGTCTGGTGGAGGTAAAGGGGTTTGTACGGCGCTTGCTATCTCCAACGCCATCACCAATCTCTCTGgt-accatctcaatcttcttccctttttgttagttggtatatatagtaggggtttctagtttt--ttaataaggctagtgtccacacag------------
||||| || |||||||| ||||| || || || ||||||||||| || |||||||| ||||| || ||||| |||||||| || || ||||||||||||||| |    |||  || | | |   ||    || ||  | |  | | |   | |    |  |||   ||  |   || ||      | |             
GAGAGGTTCGCTAAGCTGCTTCTGGGAGAGGATATGTCTGGTGGTGGAAAAGGGGTGTGTACTGCACTTGCAATCTCCAATGCAATAACCAATCTCTCTGgttagtgactctctcatgtgctaatta-actaattaatttgcacaatgtcgttgataaaatttgactaccagcacttgtaaaagaagaaaaataacatgtt

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv03s0038g03620.t01 (Vitis vinifera), 5'ss of exon 3
GAGAGATTTGCTAAGCTACTTCTCGGGGAAGACATGTCTGGTGGAGGTAAAGGGGTTTGTACGGCGCTTGCTATCTCCAACGCCATCACCAATCTCTCTGgtaccatctcaatcttcttccctttttgttagttggtatatatagtaggggtttctagttttttaataaggctag-tgtccacacag-------------
||||||||||||||||| || || |||||||| |||||||| ||||| |||||||||||||| || ||||| ||||| ||||||||||| ||||||||||||    |  || |||  |||  ||  |  |  |  ||||   |  |  |    |  ||       | |   |||| |||   ||  |             
GAGAGATTTGCTAAGCTTCTACTTGGGGAAGATATGTCTGGAGGAGGGAAAGGGGTTTGTACTGCCCTTGCCATCTCAAACGCCATCACAAATCTCTCTGgttagtttgcagtctctttctgttacttatcctgtgtatggttcctgagaaaatggaggaaaaggaaagaactagatgttttcagtgttgtgtttcctgt

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ20829 (Selaginella moellendorffii), 5'ss of exon 1
GAGAGATTTGCTAAGCTACTTCTCGGGGAAGACATGTCTGGTGGAGGTAAAGGGGTTTGTACGGCGCTTGCTATCTCCAACGCCATCACCAATCTCTCTGgtaccat-ctcaatcttc-ttccctttttgt----------tagttggtatata-tagtaggggtttctagtt---ttttaataaggctagtgtccacacag--------------------
||||  ||||| ||||| ||||| || ||||||||||| || || |  ||||| ||||| || ||||| || || |||||||||||||| |||||  ||||||   | ||  || |    || || |||||          | | | |  |||| | |||| | |  | || |   ||||  |   | | |  |                            
GAGAAGTTTGCGAAGCTTCTTCTTGGAGAAGACATGTCCGGAGGCGCCAAAGGCGTTTGCACAGCGCTCGCGATTTCCAACGCCATCACAAATCTTGCTGgtagagtacttgatttgagctctctctttgtcctcgtactctggcttggctatacttgtagagctgacgagctaccttttgtttttgttggcttgtttttttttttcttctttacgatacag

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ32418 (Selaginella moellendorffii), 5'ss of exon 1
GAGAGATTTGCTAAGCTACTTCTCGGGGAAGACATGTCTGGTGGAGGTAAAGGGGTTTGTACGGCGCTTGCTATCTCCAACGCCATCACCAATCTCTCTGgtaccat-ctcaatcttc-ttccctttttgtt-----------agttgg-tatatatagtaggggtttctagtt---ttttaataaggctagtgtccacacag----------------------
||||  ||||| ||||| ||||| || ||||||||||| || || |  ||||| ||||| || ||||| || || |||||||||||||| |||||  ||||||   | ||  || |    || || ||||||             |||| ||||  | |||| | |  | || |   ||||  |  || | |  |                              
GAGAAGTTTGCGAAGCTTCTTCTTGGAGAAGACATGTCCGGAGGCGCCAAAGGCGTTTGCACAGCGCTCGCGATTTCCAACGCCATCACAAATCTTGCTGgtagagtacttgatttgagctctctctttgttttcgtactctggcttggctatacttggtagagctgacgagctacctttttttttggttggcttgtttttttttttttcttcttcacgatacag

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|86067298|gb|DR363055.1|DR363055
EST:     AGGGGTTTGTACGGCGCTTGCTATCTCCAACGCCATCACCAATCTCTCTG                         CGACTGTGTTTGGCGAACTATGGAGGCTTGAGCCTCTTGCTCCTCAGAAGA
genomic: AGGGGTTTGTACGGCGCTTGCTATCTCCAACGCCATCACCAATCTCTCTGgtaccatctc ... gtccacacagCGACTGTGTTTGGCGAACTATGGAGGCTTGAGCCTCTTGCTCCTCAGAAGA