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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacaaagacgcaatcagattgtttttttttattagtgaaacaattttccaaattcgatctaaattgtttctttggtttgaaatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCTATGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGG

Basic information

species Arabidopsis thaliana
transcript AT2G03120.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g02530.2 (Oryza sativa), 3'ss of exon 3
-----------------------------gtaagacaaagacgcaatcagat--tgtttttttttattagtgaaacaattttccaaattcgatc----taaattgtttctttggtttgaaatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCTATGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGG
                              |    | |     |     | |  |  | |  |   ||  | | | |||||||   ||  |       ||| ||| ||| |   ||||   |  |||||||||| ||||| || || ||||| ||||| || || ||||| || ||||||||||||||||| || ||| |  | |||||||||||||| || |||||||
gtaagcaatatgcttcagtttgttttgttatctaccgagccatctgctgggtgctaatgtgataggttgttcacaaaattttctgcatatggctagaataacttgattcctgcatttgttcttatgtagGAGACAATGTCCAAGGAGCATGCTATGCGGTTTCCTTTGGTGGGAAGTGCTATGCTTCTCTCTCTGTTCCTTCTATTCAAGTTTCTCTCGAAAGACTTGG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g36070.2 (Oryza sativa), 3'ss of exon 3
----------------------------------gtaagacaaagacgcaatcagattgtttttttttattagtgaaacaattttccaaattcgatctaaattgtttctttggtttgaaatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCTATGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGG
                                  |   | ||   | |  || || || ||  |     ||  | | |      ||    |  ||  ||| ||  || ||||  ||    |  | |||||||| ||||| ||||||||||| ||||| || || ||||| || |||||||||||| | || || ||| |  | ||||||||||||||||| || ||||
gtaagcaatatgcttgaacttgttttatccatctgctgggcactaatgtgat-aggttattcatccaacttcct-acatgtacctctggctctgaa-taacttaatt-tttgcctttttcttatatagGAGACAATGTCCAAAGAACATGCTATGCGGTTTCCTTTGGTGGGAAGTGCTATGCTTTTGTCCCTCTTCCTTCTATTCAAGTTTCTCTCAAAAGATTTGG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G150251_T01 (Zea mays), 3'ss of exon 3
gtaagacaaagacgcaatcagattgtttttttttattagtgaaacaattttccaaattcgatctaaattgtttctttggtttgaaatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCTATGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGG
|||||  | |   |  |    ||    ||  | |  | ||||        ||      | | || | ||||||||    ||    ||  || ||||||| ||||| || || ||||| ||||| ||||| || ||||| |||||||||||| | ||||| ||  |  | ||||||||||||||||| |||||||
gtaagtaatatgtgtcaatgtatctgcttgctattcttgtgacttgtaactcatgtgaccaactgatttgtttctgcaatt--gtattatgcagGAGACCATGTCCAAGGAGCATGCGATGCGGTTCCCCTTAGTTGGAAGTGCTATGCTTTTATCACTGTTTCTTCTATTCAAGTTTCTCTCAAAAGACTTGG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 3
gtaagacaaagacgca-atcagattgtttttttttattagtgaaacaattttccaaattcgatctaaattgtttctttggtttgaaatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCTATGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGG
|||||  | | |||   ||     || |   | ||| || |||        ||      | | || | |||||| |    |||    |  |||||||||| ||||| || || ||||| ||||| ||||| || ||||| || ||||||||| | ||||| ||| |  | ||||||||||||||||| || ||||
gtaagcaatacacgtttatgtatctgatgcctattacta-tgacttgtaagtcatgcgaccaactgatttgtttttgcaatttttgtta-tgtagGAGACCATGTCCAAGGAGCATGCTATGCGGTTCCCTTTAGTTGGAAGCGCTATGCTTTTATCACTGTTCCTTCTATTCAAGTTTCTCTCAAAAGATTTGG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G08620.3 (Glycine max), 3'ss of exon 3
gtaag--acaaagacgcaatcagattgtttttttttattagtgaaacaattttccaaattcgatct----aaattgtttctttggtttga----aatggt---gtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCTATGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGG
|||||     |        | |   | || ||| |  |  ||    |    | | | ||  ||| |     ||| || |  ||| | ||     ||||||   | ||||||| ||||| || ||||||||||||||||| || || ||||||||||| ||| |  | |||||||||||| | ||||||||| | || ||||||||||
gtaagtagtgattctctgcttatcctattctttgtattgtgtttttcgtggtccaagatatgatttccgtgaatcgtgttgttgatgtgttgctaatggttttgcagGAGACAATGTCCAATGAACATGCCATGCGTTTTCCCTTTGTTGGGAGTGCAATGTTATTGTCACTTTTCTTACTCTTCAAGTTTTTATCTAAGGACTTGG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 3
gtaagacaaagacgcaatcagattgtttttttttattagtgaaacaattttccaaattcgatct----aaattgtttctttggtttga-------aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCTATGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGG
|||||       |    | |   | || |||    |  ||    ||   ||| | ||  ||| |     ||| || |  ||| | ||         ||  || ||||||| ||||| || ||||||||||||||||| || || ||||||||||| ||| |  | ||||| |||||| | ||||||||||| || ||||||||||
gtaagtagtgatcctgcttatcctattctttgcgctgtgtttttcatggttcaagatatgatttctgtgaatcgtattgttgatatgttgctaacgattttgcagGAGACAATGTCCAATGAACATGCCATGCGTTTTCCCTTTGTTGGGAGTGCAATGTTATTGTCACTCTTCTTACTCTTCAAGTTTCTATCCAAGGACTTGG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 3
gtaaga-caaagacgcaatcagattgtttttttttattagtgaaacaattttccaaattcgatctaaattgttt---ctttggtttga--aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCTATGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGG
|||||| |||  |  |||     |   ||| || | |   ||  | | |||||   ||||     |   |||      |||| | ||   | |  || ||||||| ||||| || |||||||| ||||| || || || ||||||||||| |||||  | ||||| ||| |  | ||||||||||| ||||| |||||||
gtaagaacaattagccaagttcctgcctttcttatttctatgccatatttttcatgattctggaaagcctgtccgaattttgatatgttcattcatgcagGAGACAATGTCTAATGAACATGCTATGCGCTTTCCTTTTGTTGGGAGTGCAATGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGG

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|164105950|gb|ES164723.1|ES164723
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGA
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGA
EST: gi|116442939|gb|EG485531.1|EG485531
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGAACATGCCATGCGTTTCCCACTGGTTGGGAGTGCT
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
EST: gi|86050554|gb|DR346309.1|DR346309
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
EST: gi|86050556|gb|DR346311.1|DR346311
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGCTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
EST: gi|125301056|gb|EL315141.1|EL315141
EST:     TTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAAGAACATGCCATGCGTTTCCCNTTGGTTGGGAGTGC
genomic: TTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAA-GAACATGCCATGCGTTTCCCATTGGTTGGGAGTGC
EST: gi|86050548|gb|DR346303.1|DR346303
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
EST: gi|86050557|gb|DR346312.1|DR346312
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
EST: gi|86050552|gb|DR346307.1|DR346307
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
EST: gi|86050550|gb|DR346305.1|DR346305
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGCTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
EST: gi|163983735|gb|ES148641.1|ES148641
EST:     CACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAAACG                         GAGACGATGTCAAAAGAAC
genomic: CACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAA-CGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAAC
EST: gi|86050551|gb|DR346306.1|DR346306
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
EST: gi|86050547|gb|DR346302.1|DR346302
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
EST: gi|86050549|gb|DR346304.1|DR346304
EST:     TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACG                         GAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT
genomic: TCACTGTTTATGTGGGTTGCTTTCGTTCGGTCAAGGATACTCCTCCAACGgtaagacaaa ... aatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaacaattttccaaattcgatctaaattgtttctttggtttgaaatggtgtagGAGACGATGTCAAAAGAACATGCCATGCGTTTCCCATTGGTTGGGAGTGCTATGCTTCTCTCACTTTTCTTATTGTTCAAGTTTCTCTCAAAGGACTTGG
                     atctaaa  putative branch site (score: 3)
                        taaattgtttcttt  TA-rich tract