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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctgacttgtctcttatcagtctgaatgtactactaatttagtctcatgagtaatctcctattgtactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgtaatgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA

Basic information

species Arabidopsis thaliana
transcript AT3G59110.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g47470.1 (Oryza sativa), 3'ss of exon 3
gtgagtctgacttgtctcttatcagtctgaatgtactactaatttagtctcatgagtaatctcctattgtactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgtaatgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA---
     |   | || | |    ||  |     || |  |  ||| | || |  |   |  || | | || |   || | | |   || | | |    |||  |  |               ||||||||||||| ||||| ||||| || | ||| ||| ||||||||||||| ||||| |||||| |        |||  || ||||||||    || |||||    
----atggaaattctgttccttccctt---gtgcataatcaatat-gtgttttccttgttcccttgtt-tctcactgtacattgaccttttctgaatattcacct---------------gcagGATGCTTGTCTATGAATATGTCAACAATGGAAACCTAGAACAATGGCTTCATGGGGCCATGAGTGGG---GGCATCCTTACTTGGGAAAACCGTATGAAGATT

upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 3
gtgagtctgacttgtctcttatcagtctgaatgtactactaatttagtctcatgagtaatctcctattgtactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgtaatgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA
                  |||   ||   | ||   | | ||| |    |  ||   |   | ||||  |  |   |  ||  ||  | |||    |||||   ||||  ||| | || | |||||||||||| || || ||||||||||  || ||||||||||| ||||| ||||| |||||| |  ||||  |   ||| || ||||| || || ||||||
------------------ttagtggtt--agtggtgtccaaatctttctttgtgtacatcatactatgtttttgtagtctattaaact-tccatcctatca---tctgacttgttatattccagGATGCTTGTATACGAATATGTGAATAACGGGAACTTAGAACAGTGGCTTCATGGTGCCATGCGCCAACATGGTGTTCTTACCTGGGAAGCCCGAATGAAA

upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G010953_T01 (Zea mays), 3'ss of exon 1
gtgagtctgacttgtctcttatcagtctgaatgtactactaatttagtct-catgagtaatctcctattgtactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgtaatgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA
                   ||      || ||| || || | |  | | |  |||  | || | | ||  |  ||   |||  |   || |  | |    | | |  | |  || | |  | |||||||||||| || ||||||||||||| ||| ||||||||||| ||||| ||||| || ||| |  | ||  |   ||| ||||||||||| || ||||||
-------------------taaagtggtgtatggac-accattcaaatatatatgcttcatatgccatattgttatttaatcta---ttttagcgttctcctaatcatatcatgttat--tccagGATGCTTGTGTACGAGTATGTGAATAATGGGAACTTAGAACAGTGGCTTCATGGTGCAATGCGTCAGCACGGTGTTCTTACTTGGGAGGCCCGGATGAAA

upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 3
gtgagtctgacttgtctcttatcagtctgaatgtactactaatttagtctcatgagtaatctcctattgtactaccgaatagaaacttgtccca-tgtatcaatttctgttttgatgtaatgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA
                    |   ||   ||| || ||| |    | ||| ||  ||  ||    ||  || ||  |  |   ||  | |   | |||    |||    | |     || | |||||||||||| |||||||| ||||| | ||| || |||||||| ||||| ||||| |||||| |  | ||  |   ||| |||||||| || || ||||||
--------------------agtggtt--aatatattaccatggaaatct-atatgtt-tcatacatcata-tattgttttttaatctatttgagtgttctcattatcatatcctcttactccagGATGCTTGTGTATGAGTACGTGAACAATGGAAATTTAGAACAGTGGCTTCATGGTGCCATGCGTCAGCATGGTGTTCTTACTTGGGAAGCCCGGATGAAA

upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G031400_T01 (Zea mays), 3'ss of exon 3
gtgagtctgacttgt-ctcttatcagtctgaatgtactactaa--tttagtctcatgagtaatctcctattgtactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgtaatgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA---
           | ||  |  |  ||     || | | |   ||  || |  ||  || | | | |  | ||||  |   | |||   |||||| |        ||| | || ||         ||||||||||||| || |||||||| |||| ||| ||| | ||||||||||| |||||   | ||    ||||  |    || | ||||||    || ||||||   
-----------tagtatttctggcaacaaaaaggcaatttcaaggttcaaactattgtg-attatatttttgttttgttgcatatggacttgttctg------aatatttgctt---------gcagGATGCTTGTCTACGAGTATGTTAATAATGGCAACCTGGAACAATGGCTTCATGG---CGTGAATCAACACGGTGTCCTTAGTTGGGAAAACCGTATGAAAATT

upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 2
---------------------------------------gtgagtctgacttgtctctta---tcagtctgaatg-tactactaa-tttagtctcatg--agtaatctcctattgtact----accgaatagaaacttgtccc------atgtatcaatttctgttttgatgta-----------------atgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA
                                          | | ||  || | |   |   ||| ||| |||  || | | |  ||| |  | |||  ||| || | ||| |         |  | | | || ||| || |      |||| ||  | |||||  | ||| |                 || |||| ||||||| ||||| |||||||| | ||||||||||||||||||| ||||||||| ||||    || |  | || || || |||||||| |||||||||
gtaaaaaatattctttgttttcctacattagtatccactaacactttgtattatattgcacattcattctcaataatagtgccagctttgggtttatgatagtcatattctacttagtccgaaattggacataagcttttctctgtgttatgtctctttatctgtcataatgaatgtgcttcctgattgatattcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAGACATGCATCAATATGGAACACTTACCTGGGAGGCCCGCATGAAA

upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 2
---------------------------------------------------------gtgagtc---tgacttgtctcttatcagtctgaatgtactactaattt---agtctcatgagtaatctcctattgtactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgtaa--tgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA
                                                          | | ||   |  |     |  | |     |  ||||  ||||  | |   |      |||  |        ||    |     ||||    || |||  | |   |  ||  |||    | | |  |||||| |||| || ||||| |||||||| | ||||||||||||||||||||||||||| || ||| |  ||||| | || || || ||||| || || ||||||
gtaaacttggtgttcttaatgcatcaaaatatcaccaatgcatatttcccttctatactcaatcacattgcaaactttattttgtgatagatgtgttacttttctgtcaaaaatttgaacagaacatcttttccttgttatatagttctttttcctttattatagatttggttgccgtctgatttgcagGTTGCTGGTATATGAATATGTGAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCCCGGATGAAA

upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 4
gtgagtctgacttgtctcttatcagtctgaatgtactactaatttagtctcatgagtaatctcctattgtactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgta-atgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA
                       |   |  |  |  | | || ||   |  | |  |       | || |    |   |||   | |  |  |||  || ||| |   |   |||  | || |||| ||||||| ||||| |||||||| | ||||||||||||||||||| ||||||||  ||||    || |  | || || || |||||||| |||||||||
-----------------------atattctactttgtccaaaattgaacataagcttttctctatgttatgtctctatatatgtattc-tgtcata-atgaatgtgcttcccgattgatattcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA

upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------gtgagtctgactt-gtctcttatcagtctgaatgtactactaatttagtctca----tgagtaatctcctattgtactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgtaa--tgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA-
                                                         |  ||||  | |  |    |||| | | |  ||||  ||| |||  |    |||  |        ||    |     ||||    || ||     ||  || | | |||    | | |  |||||| |||| || ||||| ||||| || | ||||||||||||||||||||||||||| || ||| |  ||||| | || || || ||||| ||||| |||||| 
taagctttgtaaaaatatcacaaatgcatattttcccttctatattcgatcacattacaaactttattttgtggtggtcttagtct--tactttttttgtcaaaaatttgaacagaacatcttttccttgttatatagttctttttctttcataataaatgcggttgccgtctgatttgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCTCGAATGAAAG

upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------------------------gtgagtctgact--tgtctcttatcagtctgaatgtactactaatttagtctcatgagtaatctccta----ttgtactaccgaataga---aacttgtccc--atgtatcaattt--ctgttttgatgtaatgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA
                                                              ||  | | | |  | | | || |||   |||| |||||  |   ||         |||| | | | |    || | | | |   | ||    | ||| |    ||||    || |   | || |  | ||||  |||||||| || ||||| |||||||| | ||| ||||||||||| ||||| |||||||| ||| |  || |  |||  || ||||||||||| |||||||| 
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaa-gtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG

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|164164156|gb|ES025977.1|ES025977
EST:     CACAAGAATCTTGTAAGGCTTCTAGGATATTGCATAGAGGGTGTTAATAG                         GATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAAC
genomic: CACAAGAATCTTGTAAGGCTTCTAGGATATTGCATAGAGGGTGTTAATAGgtgagtctga ... tgtaatgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgtaatgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA
                                       ttttgat  putative branch site (score: 4)
                           tatcaattt  TA-rich tract