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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaatattatcagttacgttatttacacttctttgttattcgtaaaagggtccataaatctaaccaaattgtcacctctagACCCGGCGATACCATTTTAATAGTAGCCGGTGGGAACTATCGCGTTTCTAATATTCAGATTAAAAAGCCTCTTTGCCTG

Basic information

species Arabidopsis thaliana
transcript AT3G54480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0139g00260.t01 (Vitis vinifera), 3'ss of exon 3
gtttgtaatattatcagttacgt-tatttacacttctttgttattcgtaaaagggtccataaatctaaccaaa--ttgtcacctctagACCCGGCGATACCATTTTAATAGTAGCCGGTGGGAACTATCGCGTTTCTAATATTCAGATTAAAAAGCCTCTTTGCCTG
||| |||| |||| || || |   ||| |      |||| | ||   |   |||    |||||   |   |    ||||  | | ||| || || ||||||||| | || | ||| |||||||   |||  |  |||||||||||||| |||||||| |||||||||
gttagtaa-atta-catttgcacatatctgattccctttatcat--atggtaggcaatataaactgattgagggtttgttccatgtagGCCTGGTGATACCATTCTTATTGCAGCAGGTGGGAGTCATCTGGCCTCTAATATTCAGATAAAAAAGCCCCTTTGCCTG
















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|164164510|gb|EL976753.1|EL976753
EST:     TCTCAGCCTGGAGTTTTCCTCAACATTGAGTCAGCTGTATCTGCAGCAAG                         ACCCGGCGATACCATTTTAATAGTAGCCGGTGGG
genomic: TCTCAGCCTGGAGTTTTCCTCAACATTGAGTCAGCTGTATCTGCAGCAAGgtttgtaata ... tcacctctagACCCGGCGATACCATTTTAATAGTAGCCGGTGGG
EST: gi|19874582|gb|AU235413.1|AU235413
EST:     TCTCAGCCTGGAGTTTTCCTCAACATTGAGTCAGCTGTATCTGCAGCAAG                         ACCCGGCGATACCATTTTAATAGTAGCCGGTGGGAACTATCGCGTTTCTAA
genomic: TCTCAGCCTGGAGTTTTCCTCAACATTGAGTCAGCTGTATCTGCAGCAAGgtttgtaata ... tcacctctagACCCGGCGATACCATTTTAATAGTAGCCGGTGGGAACTATCGCGTTTCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttctttgttattcgtaaaagggtccataaatctaaccaaattgtcacctctagACCCGGCGATACCATTTTAATAGTAGCCGGTGGGAACTATCGCGTTTCTAATATTCAGATTAAAAAGCCTCTTTGCCTG
                               atctaac  putative branch site (score: 2)
                                             tcacctct  putative PPT
                           ataaatctaa  TA-rich tract