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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttacaatattctaatctacttattgtctacggatacatttgaagcttagccttatagttatttttcatatgtgagaagttacttggtttgagtgttatatatcacctaaaagcgtaattttttttacagttaggaatatacacaaactattaagttgcagttttgatgaagaatgcactgtttatttgtacatagGTTTCCCGATCTCTTGCTGCTTGCGAGGGTGCTCTTCTTGTTGTGGATGCATCCCAG

Basic information

species Arabidopsis thaliana
transcript AT5G08650.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 3
gtacttacaatattctaatctacttattgtctacggatacatttgaagcttagccttatagttatttttcatatgtgagaagttacttggtttgagtgttatatatcacctaaaagcgtaattttttttacagttaggaatatacacaaactattaagttgcagttttgatgaagaatgcactgtttatttgtaca-tagGTTTCCCGATCTCTTGCTGCTTGCGAGGGTGCTCTTCTTGTTGTGGATGCATCCCAG
                                                                                                  ||  | |    ||   |   ||   | | |||   | || | | | | |||  | |  ||||    ||   |       |  | ||| |   ||   | ||||||||||| ||||||||||||||||||||||| ||||| || || ||||| || |||
------------------------------------------------------------------------------------------------cctttcagagtgtcttggatgata--ctctgttattatcagca-tgttctcaatatttggagtt-tgattgaaacatcatgttaaatgtctgactgcttactagGTTTCCCGTTCTCTTGCTGCTTGCGAGGGTGCACTTCTGGTCGTTGATGCTTCTCAG

upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 3
gtacttacaatattctaatctacttattgtctacggatacatttgaagcttagccttatagttatttttcatatgtgagaagttacttggtttgagtgttatatatcacctaaaagcgtaattttttttacagttaggaatatacacaaactattaagttgcagttttgatgaagaatgcactgtttatttgtaca-tagGTTTCCCGATCTCTTGCTGCTTGCGAGGGTGCTCTTCTTGTTGTGGATGCATCCCAG
                                                                                          || |||||| || |      |   |   |  |  |||||  |||      |||   |||   | |  |   |  |||  |        | |||   |  ||| |   ||||||||||| ||||| ||||| || ||||| || ||||||||||| ||||| || |||
-----------------------------------------------------------------------------------------tttggagtgt-atgtgg----ttgtactatggtaatttttgtagtcc----tattttcaa--cactgggagtcgatttaaacatctttggaactacctgattggatgctagGTTTCCCGCTCTCTAGCTGCCTGTGAGGGCGCACTTCTTGTTGTTGATGCTTCTCAG
















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|125214224|gb|EL228786.1|EL228786
EST:     TTTGCCTCAACTTGATAGATACTCCAGGTCATGTTGATTTCTCTTACGAG                         GTTTCCCGATCTCTTGCTGC
genomic: TTTGCCTCAACTTGATAGATACTCCAGGTCATGTTGATTTCTCTTACGAGgtacttacaa ... ttgtacatagGTTTCCCGATCTCTTGCTGC
EST: gi|124967896|gb|EL041895.1|EL041895
EST:     CAGGTCATGTTGATTTCTCTTACGAG                         GTTTCCCGATCTCTTGCTGCTTGCGAGGGTNCTCTTCTTGTTG
genomic: CAGGTCATGTTGATTTCTCTTACGAGgtacttacaa ... ttgtacatagGTTTCCCGATCTCTTGCTGCTTGCGAGGGTGCTCTTCTTGTTG
EST: gi|124897361|gb|EH973575.1|EH973575
EST:     TTTGCCTCAACTTGATAGATACTCCAGGTCATGTTGATTTCTCTTACGAG                         GTTTCCCGATCTCTTGCTGCTTGCGAGGGTGCTCTTCTTGTT
genomic: TTTGCCTCAACTTGATAGATACTCCAGGTCATGTTGATTTCTCTTACGAGgtacttacaa ... ttgtacatagGTTTCCCGATCTCTTGCTGCTTGCGAGGGTGCTCTTCTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaaactattaagttgcagttttgatgaagaatgcactgtttatttgtacatagGTTTCCCGATCTCTTGCTGCTTGCGAGGGTGCTCTTCTTGTTGTGGATGCATCCCAG
                    ttttgat  putative branch site (score: 4)
                                        tttattt  putative PPT
                                        tttatttgtacata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttacaatattctaatctacttattgtctacggatacatttgaagcttagccttatagttatttttcatatgtgagaagttacttggtttgagtgttatatatcacctaaaagcgtaattttttttacagttaggaatatacacaaactattaagttgcagttttgatgaagaatgcactgtttatttgtacatagGTTTCCCGATCTCTTGCTGCTTGCGAGGGTGCTCTTCTTGTTGTGGATGCATCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT