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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatactagctgcacctcaaggttattatgtgtttagctcctacaatttagtggtgacttctgatgtaatgattctgtttgcacacatttcttccgcagTTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAACTGGTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAA

Basic information

species Arabidopsis thaliana
transcript AT1G17720.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 1
-----aatatactagctgcacc--tcaaggttattatgtgtttagctcctacaattta-gtggtgacttctgatgtaatgattctgtttgcacacatttcttccgcagTTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAACTGGTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAA
     | | | | ||    |    |  |  | ||||| |       |  | || || | |||     |||  |  || | |  |  |||      ||||||||   ||| || || ||||| || || |||||||| ||   ||| || ||||| || |||||||| ||||| || ||||||||||| |||||| |||||||||| ||
tgtggagtcttccagtattagtgattgacataattatattagctattgttgcagttaatgtgtaagtttcctaattatttacccaattt-----tatttcttc---agTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAACGGACAGATACAAA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 1
aatatactagct-gcacctcaaggttattatgtgtttagctcctacaatttagtggtgacttctgatgtaatgattctgtttgcacacatttcttccgcagTTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAACTGGTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAA
| | |  | |   |          ||| | | ||| | | |     || |  | |  || | ||  | |  |   |     ||      ||  ||  |||||||| || ||||| || || || |||||||||  ||| ||||| || || |||||||| ||||||||||| || ||||| ||||| ||||| ||||| ||
actttgttgggaagtgtggtttttttagtgtatgtattgttggatgaaatctgcga-gattcctattttctttgcttctaatgtggtgtttcattttgcagTTGATATTATTTCTGCAATTGAGTTTGATAAATCTGGTGACCACCTTGCTACTGGTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 1
aatatactagctgcacc-tcaaggttattatgtgtttagctcctacaatttagtggtgacttctgatgtaatgattctgtttgcacacatttcttc---cgcagTTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAACTGGTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAA
| |  |     |  | | || || |||||   | |           | |    ||  |       || |    |  |    |  |  |||||        ||||||||||| || || ||||| || || ||||||| |||||| ||| | |||||||| ||||| || || ||||| ||||| ||||| || || |||   | 
agtgaagggttttgatcgtcgagtttatttcatctgggagatgggtattcatatgtcg----tcaatctctgaaccccaaattgatccattttgatgaatgcagTTGACATTATCTCGGCCATTGAGTTCGATAAAACTGGAGAGCATTTGGCAACTGGAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAG

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|116411283|gb|EG453875.1|EG453875
EST:     ATTCTCTCAGGTCTTCGGTGAGCGAACCGCCGGAGAAGAAGTTCAGGAAG                         TTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAA
genomic: ATTCTCTCAGGTCTTCGGTGAGCGAACCGCCGGAGAAGAAGTTCAGGAAGgtaattattg ... tcttccgcagTTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAA
EST: gi|116432328|gb|EG474920.1|EG474920
EST:     ATTCTCTCAGGTCTTCGGTGAGCGAACCGCCGGAGAAGAAGTTCAGGAAG                         TTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAA
genomic: ATTCTCTCAGGTCTTCGGTGAGCGAACCGCCGGAGAAGAAGTTCAGGAAGgtaattattg ... tcttccgcagTTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAA
EST: gi|116478422|gb|EG521014.1|EG521014
EST:     ATTCTCTCAGGTCTTCGGTGAGCGAACCGCCGGAGAAGAAGTTCAGGAAG                         TTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAA
genomic: ATTCTCTCAGGTCTTCGGTGAGCGAACCGCCGGAGAAGAAGTTCAGGAAGgtaattattg ... tcttccgcagTTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttagtggtgacttctgatgtaatgattctgtttgcacacatttcttccgcagTTGACATCATTTCAGCCATCGAATTTGATAAAAGTGGAGACCATCTCGCAACTGGTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAA
              ttctgat  putative branch site (score: 3)
                                         catttcttcc  putative PPT
                      taatgatt  TA-rich tract