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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatctcattggaaaaattcaggactagtgttaataacaacagtgttctcatttcgtatttgtttttgataattgtag

Basic information

species Arabidopsis thaliana
transcript AT1G67430.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 5'ss of exon 6
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatctcattggaaaaattcaggactagtgttaataacaa--cagtgttctcatttcgtatttgtttttgataattgtag-------
|||||||||||  ||| |||||||||||| | ||  |||||||||||||||| || || || ||||||||| | |  || |   |    | || || | ||        | |||   |       |||| |  |||  ||     |  |  | | |||         
CTTACATGTCCTCCCCGTGCCACATTGAGCTTATCCTGTCAGAGAAGGAAGAACCAGTGAAGAAAGAGgta-tgtgcatctgtacc---ttgagaagtccattgtataagctaactgctggttgatgtttttttttattaccatctgattgtgaatgtgttatgcag

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G702426_T01 (Zea mays), 5'ss of exon 6
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatat-ttcatctcattggaaaaattcaggactagtgttaataaca-acagtgttctcatttcgtatttgt-ttttgataattgtag----------------------------------------------------------------------------
|||||||||||  ||| |||||||||||| ||||| |||||||||||||||||||||| || ||||||||| |  | ||  ||||   | ||  ||     ||   |  | | | || |   || || ||| |||||  |  ||| || |  |  | |||                                                                             
CTTACATGTCCTCCCCTTGCCACATTGAGCTGATTCTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAGgtatttaacatgctcataaaaatgccaa---ctagatattttctgagtatcttgcattgatctaatttcagagctgtattgttcttctggtacagaagtatccttccattttatgttctttccatttgaatagtatctgtctgtaatatatgtcatctttattttgtag

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G148744_T01 (Zea mays), 5'ss of exon 6
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatat-ttcatctcattggaaaaattcaggactagtgttaataacaacagtgttctcatttcgtatttgtttttgataattgtag----------
| |||||||||   || |||||||||||| |||| ||||||||||||||||||||||| || ||||||||| || | || ||||||  ||   |   ||  |    |  ||   ||     || || ||| |||||  |  | ||||||      ||            
CCTACATGTCCTCACCTTGCCACATTGAGCTGATCTTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAGgtattacacatgttcatcaaatgccatctatatattttttctgagcatcttg-cattggtctaatttcagagctatttttggcttaggttcttatggtaca

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G127521_T01 (Zea mays), 5'ss of exon 5
--------------------------------CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgta-----atatatatttcatctcattggaaaaattcaggactagtgtta----ataacaacagtgttctcatttcgtatttgtttttgataattgtag
                                |||||||||||  |||||||||||| ||| | || ||||| |||||||||||||| || || |||||||||     | || |  ||     || ||    |  | |  ||  |  |||    ||   |  | |||| |  | | ||  |   |  |     ||  ||
AGCTTAACATTCTGTTTGCCTACCTGGTCCAGCTTACATGTCCTCCCCATGCCACATCGAGCTCATCTTGTCGGAGAAGGAAGAGCCAGTGAAGAAAGAGgtatgtggacatgtggttgtgtacactgttgcacctgattacctgatttagtgcatgggattaatgttgtgctattgtggtcaatcgtttccttttcag

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 5
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatctcattggaa---aaattcaggact--agtgttaataacaacagtgttctcatttcgtatttgtttttgataattgtag
|||||||||||  ||| |||||||| ||  | || |||||||||||||||||||| || || ||||||||| |   | ||  |     || | |    | |    ||||  |    |   |  ||   |||| |  | | ||  |  ||  |         ||
CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggttttgtacactgtttgcacctgattatctgactgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcag

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G126594_T01 (Zea mays), 5'ss of exon 5
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgta-----atatatatttcatctcattggaaaaattcaggactagtgtta----ataacaacagtgttctcatttcgtatttgtttttgataattgtag
|||||||||||  |||||||||||| ||| | || ||||| ||||||||||| || || || |||||||||     | || |  ||     || ||    | || |  ||  |  | |    ||   |  | |||| |  | | ||  |   |  |     ||  ||
CTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAGgtatgtggacatgtggttgtgtacactgttgcacttgattacctgattcagtgcatgggattaatgttgtgctattgtggtcaatcgtttccttttcag

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G119169_T01 (Zea mays), 5'ss of exon 7
--------------------------------CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatctcattggaa---aaattcaggacta-----gtgttaataacaacagtgttctcatttcgt-atttgtttt-tgataattgtag
                                |||||||||||  ||| |||||||| ||  | || |||||||||||||||||||| || || ||||||||| |   | ||  |     || | |    | |    ||||      |||  | |||      ||| ||  | | || ||| ||||  |  | |   |  
TTGCAGCTTAAGATCCTACCTACCTGGTGCAGCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggttttgtacactgtttgcacctgattatctgactgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcaggctga

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G37160.1 (Glycine max), 5'ss of exon 6
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatctcattggaaaaattcaggactagtgttaataacaacagtgttctcatttcgtatttgtttttgataattgtag
||||||||||    ||||||||||||||| |||| ||||| ||||||||||||||||| || |||||||||||  ||    ||||||  ||  || | |    |    |  |  |  |    |  |    | ||| ||| | || ||| |  ||||||
CTTACATGTCATCTCCATGCCACATTGAGCTGATATTGTCTGAGAAGGAAGAGCCTGTGAAGAAAGAGgtaatg-attgaccatctctctgttaacagtatatatacttcctcttttcttttgcatca--aattcttatctattattgttc-ttgtag

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA18G01110.1 (Glycine max), 5'ss of exon 6
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatctcattggaaaaattcaggactagtgttaataacaacagtgttctcatttcgtatttgtttttgataattgtag
||||||||||    ||||||||||||||| |||| || || |||||||||||||| || || || ||||||||  ||    ||||||  ||  || |||    | |    |            ||     | ||| ||| | || ||| |  ||||||
CTTACATGTCATCTCCATGCCACATTGAGCTGATATTATCTGAGAAGGAAGAGCCGGTGAAGAAGGAGgtaatg-attgaccatctctctgataacatt--atattgacttcctcttttcttttgcatcaaattcttatctattgttgctc-ttgtag

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0010g03380.t01 (Vitis vinifera), 5'ss of exon 5
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatctcattggaaa---aattcag-----gactagtgttaataacaacagtgttctcatttcgtatttgtttttgataattgtag-------------
| || |||||    |||||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||||||  ||   ||||  |||    ||   ||  ||      ||  | | |     | |  |||   |    ||   ||| || | | |  | | | |             
CATATATGTCATCACCATGCCATATTGAGTTGATTTTGTCTGAAAAGGAAGAACCTGTTAAAAAGGAGgtaattcattagtcattgcatcaagaatagaacccaaagggagagcaatataggagaaattagttgccctggttttgattagtatcttactactcttggtgggttttgcag

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0010g03370.t01 (Vitis vinifera), 5'ss of exon 7
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatctcattggaaaaattcaggactagtgttaataacaacagtgttctcattt-cgtatttgtttttgataattgtag------------------------
| || |||||   ||||||||| || |||||||||||||| || |||||||| ||||| ||||| |||||| |  ||   ||||  |||   || |||  |   | |  |  |  || |   |||   | | || | | | | || || |  ||  ||                         
CATATATGTCATCCCCATGCCATATCGAGTTGATTTTGTCCGAAAAGGAAGAACCTGTTAAAAAGGAGgtacttaattagtcattgcatc--aagaatagaaccccaaggggagaaatataggtgaaattagttgcctttcttttgttcagcatcttatgcactactcttgttggttttgcag

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S22_76V6.1 (Physcomitrella patens), 5'ss of exon 6
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatct--------cattggaaaaattcagga-----ctagtgttaataacaacagtgttctcatttcgtatttgtttttgata-attgtag-----------------
|||||||||||   || ||||||||||| |||||| | || |||||||| | ||| || ||||||||||||||   |  || || |        ||||  | |  ||| | |        |||| |||          |||   | ||  ||||| | || ||   ||| |                  
CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgc-tgcttgatttagggtctgcattctagagtttctgtagagtttctgtgtcaatttatttgactttcgagtgtcaaatttgatgttaatgtgttgcatggttacgaactttgcag

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|125281704|gb|EL295789.1|EL295789
EST:     GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAA
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAA
EST: gi|125229440|gb|EL243525.1|EL243525
EST:     GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAG
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAG
EST: gi|164213923|gb|ES183351.1|ES183351
EST:     GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAGAAAGAG                         CCGGAGACTCAGTTGGC
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGC
EST: gi|125016612|gb|EL088881.1|EL088881
EST:     CAGAGAAGGAAGAGCCTGTCAAAAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCTTTC
genomic: CAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCTTTC
EST: gi|164002507|gb|ES052037.1|ES052037
EST:     TTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAGAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAA-TCAGCAGCTTAAGCTTTC
genomic: TTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCTTTC
EST: gi|164163051|gb|ES094763.1|ES094763
EST:     ATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAGAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCT
genomic: ATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCT
EST: gi|164026842|gb|ES205978.1|ES205978
EST:     GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAGAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGT
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGT
EST: gi|163987297|gb|ES142757.1|ES142757
EST:     TTGTCAGAGAAGGAAGAGCCTGTCAAGAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCTTTC
genomic: TTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCTTTC
EST: gi|124889231|gb|EH968133.1|EH968133
EST:     ATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCTTTC
genomic: ATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCTTTC
EST: gi|124770610|gb|EH860740.1|EH860740
EST:     ATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCAGTCAAAAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAA
genomic: ATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAA
EST: gi|164066743|gb|ES210326.1|ES210326
EST:     GGAAGAGCCTGTCAAGAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGC
genomic: GGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGC
EST: gi|164031487|gb|ES201656.1|ES201656
EST:     GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAGAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAG
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAG
EST: gi|164093321|gb|ES158526.1|ES158526
EST:     GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAGAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAG
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAG
EST: gi|164217898|gb|ES110076.1|ES110076
EST:     TGATTTTGTCAGAGAAGGAAGAGCCTGTCAAGAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCTTTC
genomic: TGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAGCTTTC
EST: gi|124920752|gb|EH994437.1|EH994437
EST:     GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTC-AAAAAGAG                         CCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAG
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatata ... ataattgtagCCGGAGACTCAGTTGGCTGCCAAGTCCAAGAAATCAGCAGCTTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAGgtaatatatatttcatctcattggaaaaattcaggactagtgttaataacaacagtgttctcatttcgtatttgtttttgataattgtag

- - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - GGAAGA