Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctgtcacatacgaatttgctccacattcctcaaaaactaaactgtggtcataatcttttacttttgcttcgtatgcagCCATTGATGACACACAACGTATGATGCAAATGGGTGGGTTTGGATTTGATGCATCAAAG

Basic information

species Arabidopsis thaliana
transcript AT4G12590.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------------------------------------gtta-gctgtcacatacgaatttgctccacattcctcaaaaactaaactgtggtcataatcttttacttttgct---tcgtatgcagCCATTGATGACACACAACGTATGATGCAAATGGGTGGGTTTGGATTTGATGCATCAAAG
                                                                                           || | |||||  |    |||     ||           |  || ||  | ||||  |  | | |  | ||||   |   |||||||  | ||||| |||||||||||||||||||||||||| |||||||||||| | ||||||
gttagttatgacttgaaagctggtcacttttatatgtatacatttagttgattcatcagtttcatgaatatgaatttttacctcttgtcactatgttgtcatttttccatt-atagcaaggattgggttagttagacaatagtcaggagttgtgatgtgtgctatttttaatgcagCTGTAGATGATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAG

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------gttagctgtcacatacgaatttgctccacattcctcaaaaactaaactgtggtc-ataatcttttacttttgcttcgtatgcagCCATTGATGACACACAACGTATGATGCAAATGGGTGGGTTTGGATTTGATGCATCAAAG
                                                                       | |   |   || |   | | || |   ||||  || |    ||| |||   |   |  |  | |  |  || ||  ||||||||  | ||||| |||||||||||||||||||||||||| |||||||||||| | ||||| 
ggttagttataacatgaaagctgatttcttttatatgtatatttgaattaattcatcaatttcatgaatatgatttttactacttttcattatgttgt-catttttccatg--taagctggaatttgttgtgatgtg-tgctgttttttatgcaGCTGTAGATGATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAA-
















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|164192835|gb|EL981742.1|EL981742
EST:     CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATG                         CCATTGATGACACACAACGTA
genomic: CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtc ... tcgtatgcagCCATTGATGACACACAACGTA
EST: gi|164163679|gb|ES170176.1|ES170176
EST:     TTGTTTGGATTAAGAGGCTTTGTTCAGTCTCATTCTCGGAGATGAAAATG                         CCATTGATGACACACAA
genomic: TTGTTTGGATTAAGAGGC-TTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtc ... tcgtatgcagCCATTGATGACACACAA
EST: gi|164175339|gb|ES109634.1|ES109634
EST:     CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATG                         CCATTGATGACACACAA
genomic: CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtc ... tcgtatgcagCCATTGATGACACACAA
EST: gi|86079343|gb|DR375100.1|DR375100
EST:     CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATG                         CCATTGATGACACACAACGTATGATGCAAATGGGTGGGTTTGGATTTGATG
genomic: CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtc ... tcgtatgcagCCATTGATGACACACAACGTATGATGCAAATGGGTGGGTTTGGATTTGATG
EST: gi|124903664|gb|EH977744.1|EH977744
EST:     CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATG                         CCATTGATGACACACAACGTATGATGCAAA
genomic: CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtc ... tcgtatgcagCCATTGATGACACACAACGTATGATGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcctcaaaaactaaactgtggtcataatcttttacttttgcttcgtatgcagCCATTGATGACACACAACGTATGATGCAAATGGGTGGGTTTGGATTTGATGCATCAAAG
           aactaaa  putative branch site (score: 2)
                              tcttttacttttgctt  putative PPT
                          ataatcttttactttt  TA-rich tract