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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattctccacttgcctgatctcgtttatccatgcttattgatttcttattgcaatcaagttccaaaagtgtacatgtttagtaaccatctaagatt...

Basic information

species Arabidopsis thaliana
transcript AT5G30510.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g20100.1 (Oryza sativa), 5'ss of exon 6
GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcat--tctccacttgcctgatctcg----------tttatccatgcttattgatttcttattgcaatcaagttccaaaagtgtacatgtttagtaaccatctaagatt----
||||| ||||||||||||| |||||| ||||| || || |||||||| || ||||||||||| || ||| |  | ||||| |||||||||      ||  || ||   |||    |          ||||||     ||||| ||     | |||| | |  ||         || ||  ||  |  |  | |    |     
GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccatcatcattttattgaggctgcaaaatgaaatttatctgacattattcataagccactgcagtaacatttggctgaattaaattgtttctccctgtatctcttcacag

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM5G862107_T01 (Zea mays), 5'ss of exon 6
GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcat---tctccacttgcctgatctcgtttatccatgcttattgatttcttattgcaatcaagttccaaaagtgtacatgtttagtaaccatctaagatt--------------------
||||| ||||||||||||| |||||| |||||||| || || ||||| || ||||||||||| |||||| |  | ||||| || |||||||        | | ||||      ||    | || |  |  |||    ||| | | |||    ||    |||   |     |    ||| |   | |   |                    
GCTGATGAGATGGCTCAGATATTCAGGCAGAGAATAGCTCAGGCAGAGGCTATGGCTCGTGCTGACATGTTGAGATTCCAGCCAGAGgtattgcaaacgttcccttgttaatgctaccgtgtcaaatcacattt-catctaacttcaactgtgtgtgtaaatcatgtggctgagctaatcgaatcatcctcctgctgtacctcttcacag

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA17G04190.1 (Glycine max), 5'ss of exon 6
GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatc-attctccacttgcctgatctcgtttatccatgcttattgatttcttattgcaatcaagttccaaaagtgtacatgtttagtaaccatctaagatt--
|| |||||||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||  | ||||| ||||||||||  |||      ||   ||  |    || |  || |  ||  |  | | |       ||||    ||  | |   ||      |||  |   || |    
GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATAGCCCAAGCAGAAGCTATGGCTCGTGCAGACATGCTAAGGTTCCAGCCTGAGgtatttattggtttattatttgtccaaaattctgaat-ccaataaaagtttaagaaactgcaaggattaagtgagactataggagataa--aatgaacacaac

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA15G14550.1 (Glycine max), 5'ss of exon 6
GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatc-attctccacttgcctgatctcgtttatccatgcttattgatttcttattgcaatcaagttccaaaagtgtacatg-tttagtaaccatctaagatt
|| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||| | ||||| || |||||||  |||      ||   || ||    ||   ||     ||  |  |      ||||   ||    ||| |||   |   |  |     |||  || |  
GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAGgtatttatttgttgattatttgttcaaaatt--tcaactcaataaaaatgaagaagcaacataggattaaaggtgactaaaatacaaatggcattaaaaaaa

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA09G03660.1 (Glycine max), 5'ss of exon 6
GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatc-attctccacttgcctgatctcgtttatccatgcttattgatttcttattgcaatcaagttccaaaagtgtacatgtttagtaaccatctaagatt-----
|| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||| | ||||| || |||||||  ||| |    ||   || ||      |||    || | | |      |  ||||    |    ||| ||| ||     ||  ||     ||| |       
GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAGgtatttattttttgattatttgttcaaa---atctcgactcaataaaaatgaa--gcaacacgggattaaaggtg-actaaaatacaaatggcataaaaaaaagtc

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv05s0077g00450.t01 (Vitis vinifera), 5'ss of exon 6
GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattctccacttgcctgatctcgtttatccatgcttattgatttctta--ttgcaatcaagttccaaaagtgtacatgtttagtaaccatctaagatt
|| ||||||||||||||||||||||| |||||||| || ||||||||||| |||||||| |||||||||||  | ||||||||||||||||  ||  |  ||    |   |    ||||   |  ||    | |    |  |   ||| |||   || |||  | ||||    |  |  || | | |  
GCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtatt-ttaactgctattgtttacataattatttttttttcccaagtggaaaggtaaaaatgaagagacagaaggatgcatgagaggccataatttgacaa-

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|125028509|gb|EL100778.1|EL100778
EST:     CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG                         AGTGGACTGACGCTGAG
genomic: CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattct ... gtttgaacagAGTGGACTGACGCTGAG
EST: gi|125090188|gb|EL148276.1|EL148276
EST:     AGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG                         AGTGGACTGACGCTGAGTTCTGACGGGATACTAGGACCACTCGGAT
genomic: AGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattct ... gtttgaacagAGTGGACTGACGCTGAGTTCTGACGGGATACTAGGACCACTCGGAT
EST: gi|124946808|gb|EL022695.1|EL022695
EST:     CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG                         AGTGGACCGACGCTGAGTTCTGACGGGATACTAGG
genomic: CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattct ... gtttgaacagAGTGGACTGACGCTGAGTTCTGACGGGATACTAGG
EST: gi|124791966|gb|EH881645.1|EH881645
EST:     TCCAACCTGAG                         CGTGGACTGACGCTGAGTTCTGACGGGATACTAGGACCACTCGGATCTGAG
genomic: TCCAACCTGAGgtatcattct ... gtttgaacagAGTGGACTGACGCTGAGTTCTGACGGGATACTAGGACCACTCGGATCTGAG
EST: gi|124710165|gb|EH801567.1|EH801567
EST:     ATGCTTCGCTTCCAACCTGAG                         AGTGGACTGACGCTGAGTTCTGACGGGATACTAGGA
genomic: ATGCTTCGCTTCCAACCTGAGgtatcattct ... gtttgaacagAGTGGACTGACGCTGAGTTCTGACGGGATACTAGGA
EST: gi|125201908|gb|EL216862.1|EL216862
EST:     CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG                         AGTGGACTGACGCTGAGTTCTGACGGGATACTAGG
genomic: CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattct ... gtttgaacagAGTGGACTGACGCTGAGTTCTGACGGGATACTAGG
EST: gi|86074980|gb|DR370737.1|DR370737
EST:     CGCAAGCAGAAGCCATGGCTCGTGCAGACATG-TTCGCTTCCAACCTGAG                         AGTGGACTGACGCTGAGTTCTGACGGGATACTAGGACCACTCGGATCTGAG
genomic: CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattct ... gtttgaacagAGTGGACTGACGCTGAGTTCTGACGGGATACTAGGACCACTCGGATCTGAG
EST: gi|124881097|gb|EH959999.1|EH959999
EST:     CGCAAGCAGAAGCCATGGCTCATGCAGACATGCTTCGCTTCCAACCTGAG                         AGTGGACTGACGCTGAGTTCTGACG
genomic: CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattct ... gtttgaacagAGTGGACTGACGCTGAGTTCTGACG
EST: gi|124816013|gb|EH900879.1|EH900879
EST:     CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG                         AGTGGACTGACGCTGTAGTTCTG
genomic: CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattct ... gtttgaacagAGTGGACTGACGCTG-AGTTCTG
EST: gi|164131938|gb|ES198079.1|ES198079
EST:     CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG                         AGTGGACTGACGCTGAGTTCTGACGG
genomic: CGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattct ... gtttgaacagAGTGGACTGACGCTGAGTTCTGACGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattctccacttgcctgatctcgtttatccatgcttattgatttcttattgcaatcaagttccaaaagtgtacatgtttagtaaccatctaagatt

- - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgatct