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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcttatttgaattggttatttttgtcttgtaatgatataaatagtttatgtgctagaatttgcttagtatcattcaactaaatttgtgacttgttgtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG

Basic information

species Arabidopsis thaliana
transcript AT3G04120.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g38920.1 (Oryza sativa), 3'ss of exon 5
gtttgtcttatttgaattggttatttttgtcttgtaatgatataaatagtttatgtgctagaatttgcttagtatcattcaactaaatttgtgacttgttgtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG
                                |  | |  | |    | ||| | || |     |      |||    |   || |||      | | ||  || | |||||||||||||||||||| || || ||||| |||||||||||||| || ||||| |||||||||||||||||| | || |||||||| ||| || ||||||
-------------------------------gtacattcctgtgt-caatttttctgttcagggtcaagctgtagatctgttctcaat------catttttcatatgcagGGTGGTGCCAAGAAGGTCGTCATTTCTGCTCCCAGCAAAGACGCCCCCATGTTCGTTGTTGGTGTCAACGAGAAGGAGTACAAGTCTGACGTTAACATTG

upper sequence: AT3G04120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g03290.3 (Oryza sativa), 3'ss of exon 4
gtttgtcttatttgaattggttatttttgtcttgtaatgatataaatagtttatgtgctagaatttgcttagtatcattcaactaaatttgtgacttgttgtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG
 ||  | ||| |   |   ||  || ||||   | |      |   |  |  ||  | |||   || |   | ||  || |  |   |   || || ||| |     ||||||||||||||||||||||| ||||||||||| |||||||| ||||| ||||||||    |||||||||||| || | ||||  || ||  |||| ||||
-ttatttttactctgaaaagtacttgttgt---gcatctccct---tgttgcataagttagctatttcggtgcatttttta--tgcttacatggct-gttctgaaaacagGGTGGTGCCAAGAAGGTTGTCATCTCTGCCCCGAGCAAAGATGCTCCGATGTTTGTCTGCGGTGTCAACGAGGACAAGTACACTTCAGATATTGATATTG

upper sequence: AT3G04120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g40950.1 (Oryza sativa), 3'ss of exon 5
----gtttgtcttatttgaattggttatttttgtcttgtaatgatataaatagtttatgtgctagaatttgcttagtatcattcaactaaatttgtgacttgttgtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG
     ||   |  |    ||   || ||| ||   ||||  ||  ||||  | || || ||  |||||     |  |   ||        || || |  |   | ||      ||||||||| |||||||| || |||||||| |||||||| || || || |||||||||||||||||||| ||| | || |||||| | ||| | |||||||
gtattttctgcgaaacccaacatgtcattgtttgattgtggtgtcataa-caattcatatga-agaatgattctcatggtatc-------atatgcgtttcaatata------gGGTGGTGCTAAGAAGGTCGTCATCTCTGCTCCCAGCAAGGATGCCCCCATGTTTGTTGTTGGTGTCAATGAGAAGGAGTACAAGCCTGACATCGACATTG

upper sequence: AT3G04120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G046804_T02 (Zea mays), 3'ss of exon 5
gtttgtcttatttgaattggttatttttgtcttgtaatgatataaatagtttatgtgctagaatttgcttagtatcattcaactaaatttgtgacttgttgtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG
  | ||     || |     | | || |   ||||       |  ||  ||  | || || | |       | ||  |||   ||  |||        ||  | |  ||||||||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||||||||| ||| || | ||||  || ||  || ||||||
-ctcgttactctt-atcacatcacttctactttgtgtcagattggatt-ttcctctgttaaatt-------ggatgtttctgatagctttactttccttttgaatgacagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCAAGCAAAGACGCACCCATGTTTGTTGTTGGTGTCAATGAGGACAAGTACACCTCGGATGTTAACATTG

upper sequence: AT3G04120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G180625_T02 (Zea mays), 3'ss of exon 5
gtttgtcttatttgaattggttatttttgtcttgtaatgatataaatagtttatgtgctagaatttgctta-gtatcattcaactaaatttgtgacttgttgtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG
       |  |      |  |   |  || ||||| |    |    || | ||| | |     | |||| | | ||  |||   ||  ||| |       |  | |  ||||||||||||||||||||||||||||||||||| |||||||| || || |||||||||||||||||||| ||| || | ||||  |||||  || ||||||
-------tagtgcagtgtcatggctcatgacttgtcacttcacttttactgtattttc----gtctgctaatggatgtttctgatagctttattttcctattgaatgacagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCAAGCAAAGATGCGCCCATGTTTGTTGTTGGTGTCAATGAGGACAAGTACACCTCCGATGTTAACATTG

upper sequence: AT3G04120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G176307_T01 (Zea mays), 3'ss of exon 5
gtttgtcttatttgaattggttatttttgtcttgtaatgatataaatagtttatgtgctagaatttgcttagtatcattc---aactaaatttgtgacttgttgtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG
           |  |||    ||  |   |  ||| ||  |||    ||  ||| | |   | |   | |||| | ||     ||   |||   |  | |||||  ||| ||||||||||||||||||||||| |||||||| || ||||| || || || |||||||| ||||||||||||||| | || |||||||| ||| || ||||||
----------gtataatcatctacct--attgtgttattctatttccagggtatataccttactagtcctagtgttatggaagaatctaatggttttcctgttgcttttacagGGTGGTGCCAAGAAGGTTGTCATCTCTGCTCCTAGCAAGGATGCCCCCATGTTTGTCGTTGGTGTCAACGAGAAGGAGTACAAGTCTGACATTAACATTG

upper sequence: AT3G04120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G071630_T02 (Zea mays), 3'ss of exon 4
gtttgtcttatttgaattggttatttttgtcttgtaatgatataaatagtttatgtgctagaatttgcttagtatcattcaactaaatttgtgacttgttgtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG
                  |  || |||||| || |       || |||  ||||  | |  |   |   | | | |||  ||| |  ||     | |||||  ||| ||||||||||||||||||||||| || ||||| || ||||| || || || ||||| |||||||||||||||||| | || |||||||| ||| |  ||||||
------------------gtataattttgttttattccagggtatataccttattagttccagcat---tggaagcatctaacgatttt-----cctgttgcttttacagGGTGGTGCCAAGAAGGTTGTCATTTCTGCTCCTAGCAAGGATGCCCCCATGTTCGTTGTTGGTGTCAACGAGAAGGAGTACAAGTCTGACATCAACATTG

upper sequence: AT3G04120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G01330.1 (Glycine max), 3'ss of exon 5
---gtttgtcttatttgaattggttatttttgtcttgtaatgatataaatagtttatgtgctagaatttgcttagtatcattcaactaaatttgtgacttgttgtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG
   |    ||  |  | ||| | | |||  ||||||   || || ||   ||||||  |  |    |    | ||||| |||    ||   || |||            |||||||||||||||||||||||| ||||||||||| |||||||| || || ||||||||||||||||| |||||| | || |||||| | || ||||||||||
tttgccaatcgaaaataaatggatcattcgtgtctttagat-atctaggaagtttaattagtgatttgaaatgagtataatttggttatggttatga------------tcagGGTGGTGCCAAGAAGGTTGTCATCTCTGCCCCAAGCAAAGATGCACCCATGTTTGTTGTTGGTGTTAACGAGAAGGAGTACAAGCCAGAGCTTGACATTG

upper sequence: AT3G04120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G37360.1 (Glycine max), 3'ss of exon 5
----------gtttgtcttatttgaattggttattttt---gtcttgtaatgatataaatagt--tta--tgtgctagaat-ttgcttagtatcattcaacta------aatttgtgacttgttg--tattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG
           | | || |||||   |   ||  ||||    |||| | ||  | | |||| |  | |  |||    |||| ||  |||||   ||  ||  |      |||||  || |  | |  |||  |||||||||||||||||||||||| ||||||||||| |||||||| || || ||||||||||||||||| |||||| | || |||||| | || ||||||||||
gtttgttgtgatctctcatatttctgtcttttggtttttggatcttttgattttttgaatactaatcacctgtctaggaatattaattagtgatatgaaatgagtatataattttggattaatgggttatgatcagGGTGGTGCCAAGAAGGTTGTCATCTCTGCCCCAAGCAAAGATGCACCCATGTTTGTTGTTGGTGTTAACGAGAAGGAGTACAAGCCAGAGCTTGACATTG

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|116486292|gb|EG528884.1|EG528884
EST:     AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
genomic: AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
EST: gi|116486291|gb|EG528883.1|EG528883
EST:     AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
genomic: AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
EST: gi|47828958|gb|CK118642.1|CK118642
EST:     CTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
genomic: CTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
EST: gi|124900822|gb|EH975440.1|EH975440
EST:     AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAG
genomic: AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAG
EST: gi|164216759|gb|ES108373.1|ES108373
EST:     AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTA
genomic: AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTA
EST: gi|301501644|gb|HO207184.1|HO207184
EST:     AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
genomic: AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
EST: gi|124969687|gb|EL043574.1|EL043574
EST:     AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAG
genomic: AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAG
EST: gi|124939760|gb|EL016274.1|EL016274
EST:     AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAG
genomic: AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAG
EST: gi|124968899|gb|EL042826.1|EL042826
EST:     CTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGAACGCTCCAAT
genomic: CTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGA-CGCTCCAAT
EST: gi|125063118|gb|EL131212.1|EL131212
EST:     CACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
genomic: CACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
EST: gi|152034627|gb|BP833157.2|BP833157
EST:     AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
genomic: AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
EST: gi|164022619|gb|ES131112.1|ES131112
EST:     GTTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTA
genomic: G-TCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTA
EST: gi|124742828|gb|EH833990.1|EH833990
EST:     CTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
genomic: CTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
EST: gi|124783209|gb|EH873081.1|EH873081
EST:     GTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTACACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTAT
genomic: GTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCT-CACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTAT
EST: gi|163997218|gb|ES075012.1|ES075012
EST:     AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCC
genomic: AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCC
EST: gi|116480469|gb|EG523061.1|EG523061
EST:     AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
genomic: AGTCTACTGGTGTCTTCACTGACAAAGACAAGGCTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
EST: gi|125270837|gb|EL284922.1|EL284922
EST:     CTGCAGCTCACTTGAAG                         GGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG
genomic: CTGCAGCTCACTTGAAGgtttgtctta ... gtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctagaatttgcttagtatcattcaactaaatttgtgacttgttgtattttcagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGACCTTGACATTG
                         aactaaa  putative branch site (score: 2)
                                              tattttc  putative PPT
                     attcaactaaattt  TA-rich tract