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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctataagacaggctacatgaatgaacaatctatatatcttactctcttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA

Basic information

species Arabidopsis thaliana
transcript AT5G54590.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G36140.1 (Glycine max), 3'ss of exon 3
ctataagacaggctacatgaatga-acaatctatatatct-tactctcttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA
|| |     ||  |  | | || |   | || |||| ||| ||   ||||      || ||       | ||    | ||   ||    ||  | || |||||||||||| ||||||||||| |||||  | || || || || ||| | || || |||||||| ||||| |||||||||||| ||||||| ||||||||||
ctgttgcgaagtattaaggtatcatgtagtcaatatttctgtatgatctttccgcttgtttgccaatctaaaccttttatgttcttttatt--ttttctcagGTTATGTTGTTGGGAAGGTTACATCATAGAAATCTGGTCAATTTGGTCGGGTATTGTGCAGAAAAAGGACAACACATGCTTGTATATGTCTACATGAGTA

upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G41510.1 (Glycine max), 3'ss of exon 3
-ctataagacaggctacatgaatgaacaatctatatatcttactctcttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA
  || |   |     | ||  |   ||  ||| ||  || |    | ||| |    |  |  |||        |    |  | |   ||   | ||||||||| ||||| ||||||||||| || ||  | || || ||||| ||| ||||||| |||||||| || ||  |||| |||||| ||||||| ||||||||||
tttacagtccttatcatatacaatcactttctgtacttcctttctttttactccaagagtcattttcaattgtaacagttta-tgatctactttttttcagGTCATGTTGTTGGGAAGGTTACACCATAGAAATCTGGTGAATTTGGTTGGATATTGTGCAGAAAAGGGGAAACATATGCTTGTATATGTATACATGAGTA

upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0014g04960.t01 (Vitis vinifera), 3'ss of exon 2
ctataagacaggctacatg--aatgaacaatcta-tatatcttactctcttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA
  || |      || | |   | || | ||| || || |   |  || | |  |    |||| | || ||   | | |   | | |    ||  | || |||||||   ||| |||||||||| |||||  | ||||| ||||| ||| |||| || ||||| || || ||||| || |||||||||||||| ||||||||||
-catgaatgttcctgcctcttactgcaaaatgtaataaacacttttccccttatggtagctttgcttgttattacattaccctatttttatt--tgttctcagGTTCACTTACTGGGAAGGTTACATCATAGAAACCTCGTGAATTTGGTTGGGTATTGTGCCGAAAAGGGCCAGCATATGCTTATATATGTCTACATGAGTA

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|125088738|gb|EL147365.1|EL147365
EST:     AAGTTCTAGCCACTGATTCTAAACAGGGCGAAAAAGAGTTTCAGACAGAG                         GTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAA
genomic: AAGTTCTAGCCACTGATTCTAAACAGGGCGAAAAAGAGTTTCAGACAGAGgtaagatata ... atcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagtatctgcttagtttcttgaaaaactcatccactcgccttaatcttttcagGTTATGTTATTGGGAAGGTTGCATCACCGTAACCTAGTGAACTTGATTGGATACTGTGCAGAGAAAGGCCAACACATGCTTATATATGTTTACATGAGTA
                                        ccttaat  putative branch site (score: 4)
                                              tcttttc  CT-rich tract
                                          ttaatctttt  TA-rich tract