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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC

Basic information

species Arabidopsis thaliana
transcript AT1G52360.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttctt------ctctaatttgtagt--gttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                                                                 |  | |||| |  ||  | |   ||| |  ||||  | |  |||   ||       | | ||    | |  | |      |    |||| ||||||| |||||||| || ||||||||||||||  | ||||| |||||||| ||||||||||| ||||| | ||| 
-----------------------------------------------------------------gtgagtaattttgtt--cctggatttaaatttttttttgcgtgtcatttggaatattatgatgctaaataggatctgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                                                         || || |      | ||    |    || | |||| |  |    | |  | ||      |||| | | |     |||   | |  |||| ||||||| |||||||| || ||||||||||||||  | ||||| |||||||| ||||||||||| ||||| | ||| 
-------------------------------------------------------gtgagtaattttg-ttcatggattcaaatttattttgcgtgtcatttggaatattatgatgctaaataggatc--cgctttctta--tttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgct----acataacgttt---gcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                                                            || |||||  |  || | |     | | ||  |   |||  |    |   |    | | |  ||| |||   ||    ||||     ||   | ||||||| || |||||||||||||||||||||||| | ||||| ||||| || ||||||||||| |||||||  || 
-----------------------------------------------------------gtaatggaatttgttacctta----ttatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
gtatcccagttaacttggctcagtttattgtaa-gaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatt-tgt-agtgttgctacataacgtt-tgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                             |||| ||  |||       |     ||   | |  |  || ||  | |       | || | ||| | |     | ||||    ||      || ||  | ||  |  |  |  | || || ||||||| || |||||||||||||||||||||||| | ||||| ||||| || ||||||||||| |||||||  || 
-----------------------------gtaatgacatttgacatttgttgccttataatt--tcaaacctggttttgc-atttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 14
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcat-tgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                             || ||  ||| ||||       |  ||  |  | |||| ||    ||||| ||  || | | |      ||  |   ||    |  ||  ||||  |     |  | | |   ||    ||||| ||||||||||||||||||||||||| ||  | || || || ||  | ||||||||||| ||||| | ||| 
-----------------------------gtgagtcgtt-acttt------tgcttc-agcaatggatacc--catcatgtgtttttactct------tttttgccttaacgccactggaattgattactcttgtgcctggtgt----agAATGTATATTGGGCTGACAGTGGTGATTTGGTGACAATAGCAAGCGATTCGTCATTCTACATTTTGAAGTACAAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttg-cagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                                                |  || || || |||       | | ||| | |   || | |     |||||||   || ||  || | ||||||  | | ||| ||  || | | || ||||| || || |||||||||||||||||| ||||| | ||||||||||| ||||||||||||||  |||| | ||| 
----------------------------------------------gtaagtactttgattagg------tgacatc-tagttatctgctc----ttttcctt-cttattcgttgtttaattt--aattttgttatttatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttg-cagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                                                          | || |   |     |  ||||   ||   | ||   |||||||   || ||  || | ||||   || | ||| ||   | | | || ||||| || || |||||||||||||||||| ||||| | |||||||| || ||||||||||||||  |||| | ||| 
-------------------------------------------------------gtaagtactttgattaggtgacatttagtt--atctgctcttttcctt-cttattcattgtttaat--ataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                                                     |  |   | |    |  | | ||||  || ||| | ||    || | ||   | ||||||| |  | |||||  |     |   |   ||   ||||| || || |||||||| ||||||||| ||||  | ||||||||||| ||||||||||| ||| |||| | ||| 
----------------------------------------------------gtaagtgcttgcatgaggtgacatca--gctttctgcttttatttcttcttact-gtttcttgttaattttgt--taaaattttcttgtgt---cagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                                                     |  |   | |    |  |   ||||  || ||| | ||    || | ||   | ||||||| | |   ||  | | ||  |   |        ||||| || || |||||||| || |||||||||||  | ||||||||||| ||||||||||| ||| | || | ||| 
----------------------------------------------------gtaagtgcttgcatgaggtggcatca--gctttctgcttttatttcttcttact-gtttcttatttttgttaaatttttcttgtgt--------cagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                             ||||| |  | || | | | | | || |  |  ||||    || | |  |          |  |||  ||  |    |||| ||| | |  ||| |  | ||  | ||  |   || ||||| || ||||||||||| ||||| ||||| || |||||||| ||||| |||||||| |||||| |||| | ||| 
-----------------------------gtaagca-ctaacatgatggcctgttggctaccgtgg----tattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttct--ttttttttcacta---tttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                                                 ||| ||   ||      || || |  |||       ||| ||  ||     |        |  |  |  | ||  | | || | | |  ||  ||| |||||||| ||||||||||| |||||||||||||| || ||||| |||||  ||||||| |||||||| || | ||| 
------------------------------------------------gcatgttctcaa-----aaagcttacttcacaattaccaggttttggcca--cagagaaactaatagttcatttctttgggtggtttc--aatattt-cagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT

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|19878420|gb|AU239251.1|AU239251
EST:     ATGATTGGGCTGAATGTAGGCTGATTCAACGTATTGACGTCACTGTAAAG                         AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACA
genomic: ATGATTGGGCTGAATGTAGGCTGATTCAACGTATTGACGTCACTGTAAAGgtatcccagt ... acgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
                                        acataac  putative branch site (score: 3)
                       taatttgta  TA-rich tract