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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtctatttgttatctaatccaaaataacaagaacatttttttgctactacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT

Basic information

species Arabidopsis thaliana
transcript AT5G52920.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9
gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtctatttgttatctaatccaaaataacaagaacatttttttgctactacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT
         | ||||  ||  ||   ||  |   | | ||  || | || ||  | ||  ||| |    |   ||  |||||| |||    ||  |||| || |||||||| ||||||||||||||| |||| |||||||| ||||| |||||||| |||| ||| || |||||||| || || || ||||| ||  
---------gtctgaactc--tgaactgccatgatacccc--tgtgccttttcctcattcaattcccttttctaattacatttcttt----ctgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtctatttgttatct------aatccaaaataacaagaacatttttttgcta---------ctacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT
||  |||||       |     || ||  |       | |||| |     |  ||| | |      |  |  |  |  |     ||||||    | |         ||  ||||||| ||||| || ||||| |||||||||||||| ||||||||||| || ||| |||| ||||  || || ||||| || || || || ||||| ||| 
gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagtttttttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 9
------------gtaagccacgcctgatttccttgtc--ttgaaactctgcaccattgagtctatttgttatctaatccaaaataacaagaacatttttttg---ctactacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT
             ||      |||   ||  ||| |   || |  || |||||       | || ||||||    |||  ||||    |    |||||||||     | |  ||||||| |||||||||||||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||| ||||| |||||||||||  |  
gtttaagtcactctatttgttgccatgttgactttttatttaaccctttgcacttcctcatttaattgtta---gatctgaaatttgtattttatttttttggattcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACTCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 9
--gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtcta-tttgttatctaat---ccaaaataacaa--gaacatttttttgct-actacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT
   |||| ||  |    | |     | ||||   | || |  ||    |  | ||| | || ||||   |  |  | | |   | |  |||||||| | | |  ||||||| |||||||||||||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||| ||||| |||||||||||  |  
gtttaagtcaatctatttgttgccatgttgactttttgtataatcctttgcactttctcatttaattgtctgacctgaaatttgtatttttttttgttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACCCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 9
----gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtctatttgttatctaatccaaaataacaagaacatttttttgctactacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT
    | ||   |  |   ||  |  || |||     | |  | ||||| ||     | |||        |    ||   ||   ||||| | ||  |  ||||||| ||||||||||||||||| |||||||||||||||||||| || || |||||||| ||||||||||||||||| ||| | || |||||||| ||  
gtttgaaatttaaactcaatgactctgacttt---tttttaatcattgtgttctagttttactgttggtactgaaatgtgattttttttgtactg-tgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTTGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 9
----gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagt-ctatttgttatctaatccaaaataacaagaacatttttttgctactacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT
    | ||   |  |   ||  |  || |||     | |  | ||||| || ||| ||      |  | |  ||    ||     ||||| | ||| || ||||||| ||||||||||||||||| |||||||||||||||||||| || || || ||||| ||||||||||||||||| ||| | || |||||||| ||  
gtttgaaatttaaactcaataactctgactt----tttttaatcattgtgttctactttactgttggtactgaaatgtaattttttttttgtacta-tatagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTCGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G24270.1 (Glycine max), 3'ss of exon 5
gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtctatttgttatctaatccaaaataacaagaacatttttttgctactacagAACCATATGAGTGAGATGTTTGCATA--CCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT-------------
                                                                                    |    |  |  ||||||| ||||||||||||||| ||||  |||||||||||||||||| ||||| ||| |||| | |||| |||||||||| ||||  ||||| ||||    |              
-----------------------------------------------------------------------------------gtcaagtgttgaagaaccacatgagtgagATGTTTACATACACCATGCAACCATGATGTCTAACACCCTTAGAACCTTAACTATTGTCTTCACTAGAATGGGTTTAATGGTTGAAGAGATGTTTCTTGA

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------------gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtcta--tttgttatctaatccaa--aataacaa-gaacattt----------ttttgctactacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT
                                 |        ||||  |||   |    | |   | |  |  |   ||| ||  |||||  || | |  ||    |||||| ||| | ||          |  |    ||  ||||||||||||| || |||||||| | |||||||||||||||||| || || ||  | |||||||  ||||| ||||| ||||| ||||||||||| ||  
gtcatttaacatatcctttatatttattttaatgctgcattggccttgtttttgtaatgtaattttttaaaaaaaaaagtttaaatttgtactccattttaactgctaacaatgaatacttaccataagcttcctttctctgtagAACCATATGAGCGAAATGTTTGCTTTCCATGCAACCATGATGTCCAATACTCTCAGTACTTCAATAGTTGTTTTCACTAGAACTGGTTTCATGGCTATCC

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|124716434|gb|EH807836.1|EH807836
EST:     ACCATTACTAGCGGTGAAATGCCACCTAATCTTGGTCAAGCCTTCAAG                         AACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGT
genomic: ACCATTACTAGCGGTGAAATGCCACCTAATCTTGGTCAAGCCTTCAAGgtaagccacg ... gctactacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGT
EST: gi|124912302|gb|EH986382.1|EH986382
EST:     AACCGATTACTAGCGGTGAAATGCCACCTAATCTTGGTCAAGCCTTCAAG                         AACCATATGAGTGAGATGTTTGCATACCA
genomic: AACC-ATTACTAGCGGTGAAATGCCACCTAATCTTGGTCAAGCCTTCAAGgtaagccacg ... gctactacagAACCATATGAGTGAGATGTTTGCATACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtctatttgttatctaatccaaaataacaagaacatttttttgctactacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT
                        aaataac  putative branch site (score: 2)
                                      tttttttgct  putative PPT
                       aaaataacaagaacat  TA-rich tract