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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatgcttgtaccatccatctatttttgaggtttgattaaagcacttgtttcttgttaatgtcatgtggatctatttgcttattctgtagatttttagtgtatttctgattttgaatgttttcgccgcttttggttttcttttcttaatgatgttgttctttgagagttatagGAGAAGAGAATTGCTCAAGAAATCGCTAATCTTGAGAAAGATACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG

Basic information

species Arabidopsis thaliana
transcript AT5G52970.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G52970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g34950.2 (Oryza sativa), 3'ss of exon 2
gtatgcatgcttgtaccatccatctatttttgaggtttgattaaagcacttgtttcttgttaatgtcatgtggatctatt-tgcttattctgtagatttttagtgtatttctgattttgaatgttttcgccgcttttggttttcttttcttaatgatgttgttctttgagagttatagGAGAAGAGAATTGCTCAAGAAATCGCTAATCTTGAGAAAGATACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG
                                                               |   ||||| |  | || |  || | || ||  ||||    ||  || | || | ||   || |    |||    | | | |  |     |||| ||||||||          |||| ||  |  |   ||||||||| |   ||||||||||||||||||||| ||||||||||||  | || ||||| ||||| | ||| || |
--------------------------------------------------------------tttcaatgtgcactttttgtctttgtactctatgttttg---gtggttataatctaga---ttataatagctaggagctatgtactgaacctgattttgttctt----------agGAAAACCGTCTGCGTCAAGAAATAGAAGATCTTGAGAAAGATACAGGATACAAGTTGAGAGTTCTTGCACAAAATTATCCTGATACACCAG

upper sequence: AT5G52970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0040g01400.t01 (Vitis vinifera), 3'ss of exon 2
gtatgcatgcttgtaccatccatctatttttgaggtttgattaaagcacttgtttcttgttaatgtcatgtggatctatttgcttattctgtagatttttagtgtatttctgattttgaatgttttcgccgcttttggttttcttttcttaatgatgttgttctttgagagttatagGAGAAGAGAATTGCTCAAGAAATCGCTAATCTTGAGAAAGATACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG
                                                                         ||   |||| || |      || | |    ||| | |||   |||||      |   ||   ||         |  ||||| | |     |     | ||  ||||||||||  | || || || ||| ||||| |||| || |||||||||||||||||||||||  | ||||| |||||||| |  |||||||
------------------------------------------------------------------------cattattttggttttctcagcgaatctggaagtaatgctgccattgaaacaacacaa-gcaaatgaagagaacattctaatgctat----gtggataatttgcagGAGAAGAGGCTGGCACAGGAGATCACTAATATTGAAAAGGATACAGGATTCAAGTTGAGAGTTCTAGCTCAGAACTATCCTGACACCCCTG
















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|124759979|gb|EH850109.1|EH850109
EST:     TTCACTTCTGTTATAGATGTTGCTGATTTCCTCTCTAATGGTCAG                         GAGAAGAGAATTGCTCAAGAAAATCGCTAATCTTGAGAAAGATACAGGATT
genomic: TTCACTTCTGTTATAGATGTTGCTGATTTCCTCTCTAATGGTCAGgtatgcatgc ... agagttatagGAGAAGAGAATTGCTCAAGAAA-TCGCTAATCTTGAGAAAGATACAGGATT
EST: gi|125136807|gb|EL176837.1|EL176837
EST:     AAGAGTTCACTTCTGTTATAGATGTTGCTGATTTCCTCTCTAATGGTCAG                         GAGAAGAGAATTGCTCAAGAAATCGCTAATCTTG
genomic: AAGAGTTCACTTCTGTTATAGATGTTGCTGATTTCCTCTCTAATGGTCAGgtatgcatgc ... agagttatagGAGAAGAGAATTGCTCAAGAAATCGCTAATCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcgccgcttttggttttcttttcttaatgatgttgttctttgagagttatagGAGAAGAGAATTGCTCAAGAAATCGCTAATCTTGAGAAAGATACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG
                        tcttaat  putative branch site (score: 3)
                ttttcttttcttaat  TA-rich tract