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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggcctgtgtcttaagatgagtgagtgattcaatgttgctaaatgtgaggacattgatgtaactactgttatctgatgtttatccaatggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT

Basic information

species Arabidopsis thaliana
transcript AT3G12050.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G12050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G038108_T01 (Zea mays), 3'ss of exon 2
atggcctgtgtcttaagatgagtgagtgattcaatgttgctaaatgtgaggacattgatgtaactactgttatctgatgtttatccaat---ggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT
       || |   || |||     |   || ||  |    |||| ||     ||||||||     ||  ||  |    | ||| |       |    ||||| || |||||| | |||||||| || ||||| |||||||| ||||||||||| ||||||||  |||| ||||   | || || ||||| || | ||     
-------gtatgccaatatgctcacgcc-ttaaacatc---aaatatgc---tattgatgttgtctcttgtacttacaatctattcgccttgagcaattgcagGTATGGGAATTCAACTGTGGTTGAGAACACGGAGAGAGGCTGGAGAGATCTCATATTCCAGCGGATACGTGGGATGTTTGGTTTTGGGATCTAAAGAGTC

upper sequence: AT3G12050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G30230.1 (Glycine max), 3'ss of exon 2
atg-gcctgtgtcttaagatgagtgagtgattcaatgttgctaaatgtgaggacattgatgta------actactgttatctgatgt-ttatccaatggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT
 || |  | ||  | |  ||  | || || ||    |  | |   | |  |     |  |||         ||  ||  | |||| | || |  |||   |  | ||| || |||||||| ||||||||||| ||||| || || || ||| | |||||||| ||||| ||||| ||||| ||||| || |||||||| |||  || |
gtgagtgtttgattgagaatttgggaatggtttggggaagttttgtttttgttttcttttgtttggtttgttaaggtggtgtgatttgttcttgaatctgtattacagGTATGGGAATGCTACTGTGGTGGAGAACACGGAAAGGGGGTGGCGGGATCTTATTTTCCAGAGGATACGTGCTGTTTTTGGTTTTGGAATTTGAGATTTT

upper sequence: AT3G12050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G28830.3 (Glycine max), 3'ss of exon 2
atg-gcctgtgtcttaagatgagtgagtgattcaatgttgctaaatgtgaggacattgatgtaactactgttatctgat-gtttatccaatggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT
 || | | |||| | |   |    |  ||  |   ||    |   | ||   | || || || |||   | ||| || | | ||      | |   ||||||||| || ||||| ||||||||||| ||||| ||||| |||||| | ||||| || ||||| ||||| ||  | |  || |                    
gtgagtcggtgtttaatcgtttcggtttgggtt--tggaattggttttgctca-atcga-gttactgaggatatgtggttgcttgcttgcttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGATGGCGGGATCTCATTTTCCAAAGGATACGGACTGCGTTTG--------------------

upper sequence: AT3G12050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G28830.1 (Glycine max), 3'ss of exon 2
atg-gcctgtgtcttaagatgagtgagtgattcaatgttgctaaatgtgaggacattgatgtaactactgttatctgat-gtttatccaatggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT
 || | | |||| | |   |    |  ||  |   ||    |   | ||   | || || || |||   | ||| || | | ||      | |   ||||||||| || ||||| ||||||||||| ||||| ||||| |||||| | ||||| || ||||| ||||| ||  | |                          
gtgagtcggtgtttaatcgtttcggtttgggtt--tggaattggttttgctca-atcga-gttactgaggatatgtggttgcttgcttgcttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGATGGCGGGATCTCATTTTCCAAAGGATACGGACTGC-------------------------

upper sequence: AT3G12050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G28830.2 (Glycine max), 3'ss of exon 2
atg-gcctgtgtcttaagatgagtgagtgattcaatgttgctaaatgtgaggacattgatgtaactactgttatctgat-gtttatccaatggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT
 || | | |||| | |   |    |  ||  |   ||    |   | ||   | || || || |||   | ||| || | | ||      | |   ||||||||| || ||||| ||||||||||| ||||| ||||| |||||| | ||||| || ||||| ||||| ||  | |  || || |||||||| ||| ||| |
gtgagtcggtgtttaatcgtttcggtttgggtt--tggaattggttttgctca-atcga-gttactgaggatatgtggttgcttgcttgcttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGATGGCGGGATCTCATTTTCCAAAGGATACGGACTGCGTTTGGTTTTGGAATTTGAGCTTTT

upper sequence: AT3G12050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
-------atggcctgtgtcttaagatgagtgagtgat-tcaatgttgctaaatgtgag-gacattgatgtaactactgttatctgatgtttatccaatggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT
          |    || |||    ||| |  ||  | |   |||| ||||   |  | ||   |||  |     |||||      || ||    | |   | ||||||||| |||||||| || ||||| || |||||||| ||||| ||||| ||||| || ||||| | |||  | ||||| || || ||||||||||||| || |
gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttg-tggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT

upper sequence: AT3G12050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S454_1V6.1 (Physcomitrella patens), 3'ss of exon 4
--atggcctgtgtcttaagatgagtgagtgattcaatgttgctaaatgtgaggacattgatgtaactactgttatctgatgtttatccaatggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT
   || | | |   || | ||  || | |     |  ||  ||   | ||     |      || |||    |   |  || || |||  |  |   | |||||| || ||||| || |||||||||||||| || || |||||| ||||||| || ||||||| ||| ||||| ||||| || |||||  | | |  |  |
ttttgtcattttctttcaaatcggtcattttcagatagtatctgtgtttggcagtacctgccta-ctaggactgaatcgtgattttcctgttatcttt-cagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT

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|164224022|gb|ES043306.1|ES043306
EST:     TCTTACTTCACACTGACGTTCCTGAAGAGGACAG                         ATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCT
genomic: TCTTAC-TCACACTGACGTTCCTGAAGAGGACAGgttagtttta ... gttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCT
EST: gi|86087237|gb|DR382996.1|DR382996
EST:     GKAGTCACCATTGTCAATCTTMCTCACACTGACGTTCCTGAAGAGGACAG                         ATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCT
genomic: GGAGTCACCATTGTCAATCTTACTCACACTGACGTTCCTGAAGAGGACAGgttagtttta ... gttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCT
EST: gi|86080472|gb|DR376229.1|DR376229
EST:     GAGTCACCATTGTCAATCTTACTCAACACTGACGTTCCTGAAGAGGACAG                         ATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCT
genomic: GAGTCACCATTGTCAATCTTACTCA-CACTGACGTTCCTGAAGAGGACAGgttagtttta ... gttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCT
EST: gi|86080882|gb|DR376639.1|DR376639
EST:     GAGTCACCATTGTCAATCTTACTCNACACTGACGTTCCTGAAGAGGACAG                         ATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCT
genomic: GAGTCACCATTGTCAATCTTACTC-ACACTGACGTTCCTGAAGAGGACAGgttagtttta ... gttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCT
EST: gi|164120505|gb|ES004847.1|ES004847
EST:     TCTTACTCACACTGACGTTCCTGAAGAGGACAG                         ATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCT
genomic: TCTTACTCACACTGACGTTCCTGAAGAGGACAGgttagtttta ... gttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaggacattgatgtaactactgttatctgatgtttatccaatggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT
                               atgtttat  TA-rich tract