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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtagtagtaatgtcaacacttctgatattgtcatgtttcgttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG

Basic information

species Arabidopsis thaliana
transcript AT3G49010.5
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G49010.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g02510.3 (Oryza sativa), 3'ss of exon 2
-gttagtagtagta---atgtcaacacttctgatattgtcatgtttcgttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG
  || |||||  |      | ||  |  | | || ||   |  |   | | |   |||      ||   |||     |||| |  ||||   || | ||  || ||||||||||| ||||||||||||||||| || || ||||||||||| || |||||  |||| ||  | || || ||||||||||||||||||   ||
tatttgtagtcctgcatgaggcattaaattttatgtttgaagatgctgctatttcttttttacccagcatctaattttcttttggtgttggcttttgca--gCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAG

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g37970.1 (Oryza sativa), 3'ss of exon 2
-gttagtagtagtaatgtcaacacttctgatattgtcatgttt-cgttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG
 | ||| |  |  |  |  || |  | ||     |   | ||  | || || || | || |   ||  |  |    ||| || | |  | |  |  |||||  | || ||||||||||||||||||||||| || ||||| ||||| ||||| || ||  |||| ||  | || ||| | |||||||||||||||   ||
agctagcataaccacagcaaatatgtttgcgcccgcttttttcaccttatatgtgtgcattcttatgacaatcatcctttttttttcttttgttgtacagCTCGCCAGAAGAAGGCTGTGAAGATCTTCCCCCGCCCAACATCTGGCCCTCTTCGACCCATTGTTCAGTGCCAAACTTTGAAGTACAACATGAAGTCGAG

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G409407_T01 (Zea mays), 3'ss of exon 2
----gttagtagtagtaatgtcaacacttctgatattgtcatgtttcgttttaagtttac--actacaatctctttgggtcttattatgttatgttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG
     ||  | |  |     |    |  | | || |   | |  |   | | | | ||||  ||  |  |||  || |  | |  || |||||    ||  ||||  | |||||||||||||||||||| ||||| || |||||| |||| ||||| |||||  |||||||  | |||||||| |||||||||||||||   ||
gttgcttctttgccgaccacttgttatgtgtaatttctcccttatctttctcatgattactaacagctttctactttgaccctgctacgttat----tatgcagCTCGTCAAAAGAAGGCTGTGAAGATATTCCCACGCCCAACTGCTGGCCCTCTTCGCCCCATTGTGCAATGCCAGACTCTCAAGTACAACATGAAGTCGAG

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G081102_T03 (Zea mays), 3'ss of exon 2
gttagtagtagtaatgtcaacacttctgatattgtcatgtttcgttttaagtttacactacaatctctttgggtcttattatgttatgttg--tacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG
 | |  | | |   |        | ||  |  |||    ||||      | |  ||      |      |     |||   || ||||||   |   ||||  | |||||||||||||||||||| ||||| || |||||| |||| ||||| || ||  |||| ||  | |||||||| |||||||||||||||   ||
ctcaacaattgctttcattgatttacttgttatgtatgatttcccccctattgcacctgctgacaagcgtataatttaccctgctatgttctctgtgcagCACGTCAAAAGAAGGCTGTGAAGATATTCCCACGACCAACTGCTGGCCCTCTTCGTCCCATTGTTCAATGCCAGACTCTCAAGTACAACATGAAGTCAAG

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G145280_T01 (Zea mays), 3'ss of exon 2
---gttagtagtagtaatgtcaacacttctgatattgtcatgtttcgtttta-agtttacactacaat-ctctttgggtcttattatgttatgttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG
     || |  || | |||     ||       | |||    |||   |  | | ||    ||||| | ||  ||||  | | | |||||    ||||  ||||  | |||||||||||||||||||| ||||| || || ||| |||| ||||| |||||  |||| ||  | |||||| | |||||||||||||||   ||
tactataatgatattgatgaaggaaccaagatgaatgttcgcttttactcaataattgcttctacacttctaattggaccctgtaatgtt---ctgtatgcagCTCGTCAAAAGAAGGCTGTGAAGATATTCCCCCGCCCGACTGCTGGTCCTCTACGCCCCATTGTTCAATGCCAGACTTTAAAGTACAACATGAAGTCAAG

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G17370.2 (Glycine max), 3'ss of exon 1
----------------------------------------------gttagtagtagtaatgtcaacacttctgat---attgtcatgtttcgttttaagtttacactacaatctctttgggtcttattatgttatg--ttgt-----acac------agCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG
                                               ||| |     |    | || |||| | ||   |    || |  ||   || ||||  ||  |||||   | || || |  |||| || ||  | ||     ||||      |||  |||| ||||||||||| ||||| |||||  | || ||| ||||| ||||| | ||| |||| ||||| |||||||| || ||||||||||| |||||
gtaatttaacctaatctcttgctcttttttaacattgtaatacttaattaatcagtctggc-ttaatacttgtaattcaagaaacaagaatcagcttgagttgtca--acaattgttgtgtgtatctttatattttgactcgtgggtaacactttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTCTCAGGCCTATTGTTCATGGCCAGACTCTGAAATACAACATGAAAGTCAG

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G08090.1 (Glycine max), 3'ss of exon 2
----------------------------gttagtagtagtaatgtcaacactt--ctgat--attgtcatgtttcgttttaagtttacactacaatctctttgggtcttattatgttatgttg-taca----cagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG
                            ||||  | |  |  | | |  | ||     ||   || | |    | ||| |      | | |  |    |||  | | || | |      | ||  |||    ||||  |||| ||||||||||| ||||| |||||  | || ||| ||||||||||| | ||  |||| ||||| |||||||| || ||||||||||| |||||
gtaatttttaccaaaattattgctctttgttaacattgttgctataattaattaatcaatcagtttttaatacttgttatgcaagaaaagtgaatcaacttgagttattttgacacgggggtgacacattttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCAAGGCCTACTGCTGGACCTCTCAGGCCAATTGTTCATGGCCAGACTCTGAAATACAACATGAAAGTCAG

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0047g01160.t01 (Vitis vinifera), 3'ss of exon 1
gttagtagtagtaatgtcaacacttctgatattgtcatgtttcgttttaagt--ttacactacaatct--ctttgggtcttattatgttatgttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG
 | |    |  |  |||| |  ||| | ||||| | |   || ||   | ||  |   | |  ||     |||    |  | ||   | |     |   |||| || || ||||| ||||||||||| |||||||| || |||  |||||| || |||||  |||| ||||| || ||| | |||||||||||||| |||||
-tcatgtttgattttgtccagtctttt-atattttgaatatttgtaccatgtgatgctattttaactgagcttaaattggtttttcatgaaaccatctccagCTAGACAGAAGAAAGCTGTGAAGATTTTCCCTCGCCCCACTGTTGGACCACTTCGCCCACTTGTTCATGGACAAACTTTGAAGTACAACATGAAAGTCAG

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------gttagtagtagtaatgtcaac--acttctgatattg-tcatgtttcgtt-ttaagtttacactacaatctctttgggtcttatta-------tgttatgttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG
                                 |||  |  | ||  ||  ||     |  | ||| || |  |||||| || | ||| || |  ||   | |  | |  | || ||        ||||||    |   |||| ||||||||||||||||||||||||||||| || || || |||||||| || || ||| |||| ||||| || ||||| |||||||| ||||| || ||
gtagctacttaaccattttaaaatggaaatggtgtttttcct-gtcttgctaattagttggtcataatgattctgtttcattatcaagcttgc-ttattctgtgctcgcattttcttgacatgtctgttataccatctccagCTAGGCAAAAGAAGGCTGTGAAGATCTTCCCACGGCCCACGTCTGGACCACTTCGACCTATTGTCCATGGGCAAACTCTGAAGTACAATATGAAAGTTAG

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|124977541|gb|EL050852.1|EL050852
EST:     TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|124855932|gb|EH940369.1|EH940369
EST:     GTCAAGTACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTT
genomic: GTCAAG-ACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTT
EST: gi|124954575|gb|EL029658.1|EL029658
EST:     TCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: TCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|125048447|gb|EL120716.1|EL120716
EST:     TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCT
genomic: TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCT
EST: gi|125291489|gb|EL305574.1|EL305574
EST:     TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAG
genomic: TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAG
EST: gi|125222104|gb|EL236189.1|EL236189
EST:     TTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: TTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|164017344|gb|EL974819.1|EL974819
EST:     GCCAGGAAAACCNGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: GCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|152037762|gb|BP796635.2|BP796635
EST:     TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|124749000|gb|EH839130.1|EH839130
EST:     GTCAAGTACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCG
genomic: GTCAAG-ACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG
                                ttattatgttatgtt  TA-rich tract