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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacagtctctgtggaatgttattctaatggtctcactgttatgaaagacttttttgagtggagtctctctatatggttttaattgcagGTGGTATGGTTCTTCATAAAGGAGAAATAGCTGAAATGAGAACTGGTGAAGGGAAAACGCTTGTTGCTATTTTACCAGCTTATTTGAATGCATTAAGTGG

Basic information

species Arabidopsis thaliana
transcript AT4G01800.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 2
gtaacacagtctctgtggaatgttattctaatggtctcactgttatg-aaagacttttttgagtggagtctctctatatggttttaatt--------gcagGTGGTATGGTTCTTCATAAAGGAGAAATAGCTGAAATGAGAACTGGTGAAGGGAAAACGCTTGTTGCTATTTTACCAGCTTATTTGAATGCATTAAGTGG
 |  |    |    ||| | | |    |      | |      |||  ||| |  |   | || | |   | | |  ||  | ||| ||        | ||| || |||||||||||||| |||||||||||||||||||| ||||| ||||| || || || |||||| |||| |||||||||||||||||||| |||||
-ttgccttattgtggtgtactctagcccgtgctatttagtgtgtatataaatatatgcgtaagagaataatttatgaatattgttagttcgggtcttgtagGAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACTGGAGAAGGAAAGACACTGGTTGCTGTTTTGCCAGCTTATTTGAATGCATTGAGTGG

upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 2
gtaacacagtctctgtggaatgttattctaatggtctcac-tgttatgaaagacttttttgagtgg--agtctctctatatggttttaatt--------gcagGTGGTATGGTTCTTCATAAAGGAGAAATAGCTGAAATGAGAACTGGTGAAGGGAAAACGCTTGTTGCTATTTTACCAGCTTATTTGAATGCATTAAGTGG
   ||| ||| |  ||| | | |   |       | |    | ||   ||| |  | | | || ||  | | | |  |||| || ||| ||        | ||| || |||||||||||||| |||||||||||||||||||| || || |||||||| || || |||||| |||| ||||||||||| |||||||| |||||
--tacatagtgta-gtgtactctagcttgtgctatttagtgtatttataaatatatgtgtaagaggataatttattaatattgtgttagtttgggtcttgtagGAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAGGGAAGACACTGGTTGCTGTTTTGCCAGCTTATTTAAATGCATTGAGTGG

upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 2
--------gtaacacagtc-tctgtggaatgttattctaatggtctcactgttatgaaagacttttttgagtggagtctctctatatggttttaattgcagGTGGTATGGTTCTTCATAAAGGAGAAATAGCTGAAATGAGAACTGGTGAAGGGAAAACGCTTGTTGCTATTTTACCAGCTTATTTGAATGCATTAAGTGG
          | || |||  | |    | ||   |  | ||    |       | |||||  |  | ||| |      |      ||   | || ||| |||||| |||||||||||||| |||||||||||||||||||||||||| ||||| || || |||||||| ||||||||||||||||||||||||||||||||
aaatccttagatcatagttgtttagtcagtggattgtttatttatttgtaaaca-gaaagcttaatatgaatatcaagttgaatgatatctgtatttgtagGTGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGAACTGGAGAAGGAAAGACCCTTGTTGCAATTTTACCAGCTTATTTGAATGCATTAAGTGG

upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ15249 (Selaginella moellendorffii), 3'ss of exon 2
gtaacacagtctctgtggaatgttattctaatggtctcactgttatgaaagacttttttgagtggagtctctctatatggttttaattgcagGTGGTATGGTTCTTCATAAAGGAGAAATAGCTGAAATGAGAACTGGTGAAGGGAAAACGCTTGTTGCTATTTTACCAGCTTATTTGAATGCATTAAGTGG
                                       |  |    |||  |   | ||       || |  | |   ||| |  || ||||||| ||||||||||| || ||  | || ||||| |||| |||||| ||||| ||||| ||||||||| || | ||||| ||||||||||| ||||| ||
----------------------------------gtaagcaatggataaaatcaagtgtggtctccttcacagtttcgtgttcttctttcagGTGGCATGGTTCTTCACAAGGGTCAGATTGCTGAGATGAAAACTGGAGAAGGAAAAACTCTTGTTGCTGTTCTTCCAGCATATTTGAATGCTTTAAGCGG

upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ08380 (Selaginella moellendorffii), 3'ss of exon 2
gtaacacagtctctgtggaatgttattctaatggtctcactgttatgaaagacttttttgagtggagtctctctatatg------gttttaattgcagGTGGTATGGTTCTTCATAAAGGAGAAATAGCTGAAATGAGAACTGGTGAAGGGAAAACGCTTGTTGCTATTTTACCAGCTTATTTGAATGCATTAAGTGG
                                         || |  || |  |   |  ||||  |||||  |    |      ||| |  || ||||||| ||||||||||| || ||  | || ||||| |||| |||||| ||||| ||||| ||||||||| || | ||||| ||||||||||| ||||| ||
-----------------------------------------gtaagcaatggataaatcaagtgtggtctccttgacagtttcgtgttcttctttcagGTGGCATGGTTCTTCACAAGGGTCAGATTGCTGAGATGAAAACTGGAGAAGGAAAAACTCTTGTTGCTGTTCTTCCAGCATATTTGAATGCTTTAAGCGG

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|125316314|gb|EL330399.1|EL330399
EST:     AGCTTCCAAGAGAGTTCTTGGACTCAGACCTTTCGATGTGCAATTAATTG                         GTGGTATGGTTCTT
genomic: AGCTTCCAAGAGAGTTCTTGGACTCAGACCTTTCGATGTGCAATTAATTGgtaacacagt ... ttaattgcagGTGGTATGGTTCTT
EST: gi|124810867|gb|EH895733.1|EH895733
EST:     CGATGTGCAATTAATTTG                         GTGGTATGGTTCTTCATAAAGGAGAAATAGCTGAAATGAGAACTGGTGAA
genomic: CGATGTGCAATTAA-TTGgtaacacagt ... ttaattgcagGTGGTATGGTTCTTCATAAAGGAGAAATAGCTGAAATGAGAACTGGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgttatgaaagacttttttgagtggagtctctctatatggttttaattgcagGTGGTATGGTTCTTCATAAAGGAGAAATAGCTGAAATGAGAACTGGTGAAGGGAAAACGCTTGTTGCTATTTTACCAGCTTATTTGAATGCATTAAGTGG
                                           ttttaat  putative branch site (score: 3)
                                    tatatggttttaatt  TA-rich tract