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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttccaaataaaccccttcatatagtcctatacgtttagcatcaaaatatctattttcttaagataataatatttcttttatattctgatgcagATCACTGATTTGCCATTTTCTTTGTACTCAACTTTCGTGATCGAGTCTCGGCATGGGTTCAACAAA

Basic information

species Arabidopsis thaliana
transcript AT4G01320.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 4
-gtgttccaaataaaccccttcatatagtcctatacgtttagcatcaa----aatatctattttcttaagataataatatttcttttatattctgatgcagATCACTGATTTGCCATTTTCTTTGTACTCAACTTTCGTGATCGAGTCTCGGCATGGGTTCAACAAA-
 ||  | |   |      ||||  |||    |  |  |  |  |||||    ||| ||||  || | |  |   | ||  |     ||  |  || ||||||| ||||||||||| |||||| ||||||||||||| ||||| ||| | || ||||| || |||||  
ggtaatgctttttg-ttgcttctgataactgtgcatttgaattatcaatcttaatgtctacattttaataaactttattgtgtgactacctattg-tgcagaTAACTGATTTGCCCTTTTCTCTGTACTCAACTTTTGTGATTGAGGCCCGTCATGGTTTTAACAAGG

upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------------------gtgttccaaataaaccccttcatatagtcctatacgtttagcatcaa---aatatctattttctta-agataataatatttcttttatattctgatgcagATCACTGATTTGCCATTTTCTTTGTACTCAACTTTCGTGATCGAGTCTCGGCATGGGTTCAACAAA
                                                                                          ||| |     |      ||||  |||    |  |  |  |  |||||   ||||||||  || | | | |   || | |   |       | |  ||||||| || |||||||| |||||| ||||||||||||| ||||| ||| | || ||||| || || || 
gtatgcttctgacatagtaatgctgaagttttattttttggaatatttttttcttttttattactttttgggttttggcagataatgatagtgctagctttttggtgcttctgataactgtgcatttgaattatcaatctaatatctacattttaataaactttattgtgcatgactacctattgtgcagATAACAGATTTGCCCTTTTCTCTGTACTCAACTTTTGTGATTGAGGCCCGTCATGGTTTTAATAAG

upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 4
--gtgttccaaataaaccccttcatata-gtcctatacgtttagcatcaaaatatctattttcttaagataataatatttc-ttttata-ttctgatgcagATCACTGATTTGCCATTTTCTTTGTACTCAACTTTCGTGATCGAGTCTCGGCATGGGTTCAACAAA
     ||   |||  |      ||| || |  ||  |    |   ||    || |||| |||  | |    | || ||||  |||| || || |  ||||||| |||||||||||||||||| | ||||||||||| ||||| ||| | || ||||| |||||||||
ttactttttgaatggatattcacatgtatgcactggaatggttatatttgtat-tctactttaatcaagcgacaacattttgttttgtaattttcttgcagATTACTGATTTGCCATTTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA

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|86066466|gb|DR362223.1|DR362223
EST:     AAATACTGCATACTCTTTCATTCTTGGCTGGTGTTATGACATGGTCACAG                         ATCACTGATTTGCCATTTTCTTTGTACTCAACTTTCGTGATCGAGTCTCGG
genomic: AAATACTGCATACTCTTTCATTCTTGGCTGGTGTTATGACATGGTCACAGgtgttccaaa ... tctgatgcagATCACTGATTTGCCATTTTCTTTGTACTCAACTTTCGTGATCGAGTCTCGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcaaaatatctattttcttaagataataatatttcttttatattctgatgcagATCACTGATTTGCCATTTTCTTTGTACTCAACTTTCGTGATCGAGTCTCGGCATGGGTTCAACAAA
                                            ttctgat  putative branch site (score: 3)
                                 tttcttttatattct  CT-rich tract
     aaatatctattttctt  TA-rich tract