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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGTTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaatttattgaaaccttttatagttgtaccttcttttcgtatgtttgttggagtttggtataaccaattcctgttgtattctttatgtcag

Basic information

species Arabidopsis thaliana
transcript AT4G31480.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G31480.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os11g07280.1 (Oryza sativa), 5'ss of exon 2
TAATGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGTTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaa---tttattgaaaccttttatagttgtaccttct--tttcgtatgtttgttggagtttggtataaccaattcctg--ttgtattcttta-tgtcag-
 || || || |||||||| |||||||| |||||||| ||||||   ||| | || ||||||||| | |  ||||||||||| || || |||||||||||||||    | | |   || |||      ||| |  | ||  |||   | | || ||  | | |  |||   ||  | ||   || | ||||| | ||| |  
AAACGATATTCACATTGACATCATGGATTATATCTCACCTGCTACTTGTGCCGATGTTGCTTTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtagggttctttctcaagcttcagcttttgcaaatgcttgttttacaagattctttca-tgtattatttgcagctgctagattttcttcttcactgtgatc

upper sequence: AT4G31480.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
TAATGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGTTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaatttattgaaacctt--ttatagttgtaccttcttttcgtatgtttgttggagtt-tggtataaccaattcctgt-tgtattctttatgtcag----
 ||||| || ||||| || |||||||| || ||||| ||||||  |||| |||| ||| ||||| | |  ||||||||||| || ||||||||||| |||||||| |  |      |   ||  ||||||    | |  |   |   | ||     || || |       ||||  |  ||||   ||||  | |     
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtgaagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtttaaataacgggt

upper sequence: AT4G31480.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0008g02320.t01 (Vitis vinifera), 5'ss of exon 2
TAATGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGTTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaatttattgaaa---ccttttatagttgtaccttcttttcgtatgtttgttggagtttggtataaccaattcctgttgtattctttatgtcag--------
 |||||||| |||||||| ||||||||||| || || |||||||| ||| | || || || ||||||||||||||||||||||| ||||||||||||||||||| | ||  |     ||||  ||  || | ||   |  |   || |    |   |  |  |  || |  ||  |||| ||| | |||  |           
CAATGACATTCACATTGACATCATGGACTACATATCTCCTGCTGTTTGTACTGATGTGGCCTTCAGAACTATGTGGGCAGAGTTTGAATGGGAAAACAAGgtaaatcatctagctgtccttccatgattttcccaaatggtaacatctgatctaatgggtacttgaatc--tttttgtt-tataccttacatagttatttttg

upper sequence: AT4G31480.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
TAATGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGTTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaatttattgaaaccttt-tatagttgtaccttcttttcgtatgtttgttggagtttggtataaccaattcctgttgtattctttatgtcag--------
 |||||||| |||||||| ||||||||||| ||||| ||||||   ||| | || ||||| ||  | |  |||||||| ||||| || ||||||||||||||| | ||| ||  | ||| | | | |  |  ||   |||     | | |   | ||            ||    | |  || || |  ||          
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgta-tctatcgattcttttgttttgcttcaagtttcattctctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat

upper sequence: AT4G31480.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S309_15V6.2 (Physcomitrella patens), 5'ss of exon 3
TAATGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGTTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaatttattgaaaccttttat---agttgtaccttcttttcgtat-gtttgttggagt-ttggtataaccaattcctgttg-tattctttatgtcag---
 ||||| || |||||||| ||||||||||| ||| | |||||   |||| | ||  | |||||| | |  |||||||||||||| |||||||| |||||||||    | ||   | ||||||    |  |||  ||| |||||| | || |  |    | ||| |  | |   ||  | | |  |||     | ||     
GAATGATATCCACATTGACATCATGGACTACATCGCTCCTGCCTCGTGTACTGATATAGCTTTCCGCAACATGTGGGCAGAGTTTGAATGGGAGAACAAGgta-ccaagtgctcctttttattttggccgtaaattcgtttcgtttcgtatcctacgttattgattcagcattttgatctcgacattgacgctatcgaaaa

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|164156257|gb|ES117103.1|ES117103
EST:     CAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAG                         GTTGCTGTGAACACCACAATAC
genomic: CAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaatttatt ... tttatgtcagGTTGCTGTGAACACCACAATAC
EST: gi|86058808|gb|DR354565.1|DR354565
EST:     CAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAG                         GTTGCTGTGAACACCACAATACAAAACGAAAGAGAATTCCTCGACCACATT
genomic: CAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaatttatt ... tttatgtcagGTTGCTGTGAACACCACAATACAAAACGAAAGAGAATTCCTCGACCACATT
EST: gi|86086628|gb|DR382387.1|DR382387
EST:     CAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAG                         GTTGCTGTGAACACCACAATACAAAACGAAAGAGAATTCCTCGACCACATT
genomic: CAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaatttatt ... tttatgtcagGTTGCTGTGAACACCACAATACAAAACGAAAGAGAATTCCTCGACCACATT