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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttagcttttctcggcttctggttcatcatatatagtcttctccacaattattctgatgtttgtgtcgtggtttccaaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC

Basic information

species Arabidopsis thaliana
transcript AT1G29890.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 10
------------------------------------------------------gtgagttgttagcttttc--------tcggcttctggttca--tcat-atatagtcttctccacaattattctgatgtttgtgtcgtggtttccaaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC
| ||||| ||||| | | |||| || || | ||| || || || ||| | | | | | | | | |||| || || ||||||||||||| ||||||||||| ||||||| ||| ||||| |||| |||||||| || ||||||||||| || |||||||| || ||
gtaagttgcatccatcttttaccaatgcacagactttctatattgtcaagatgacatacttgtttgctttaccaactagatttgcttttgttttaaaccatgatgctgtattgatttcaaatgctgtactaactaggacttctgttcctcat-tttagGCTGGTTACCTATGGTATGAATATATCTACAGGCTAGACAAAATTACATACAACAAGTACCATCCCTACACGTCATGGATTCCTATCAC

upper sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 5
----------------------------------gtgagttgttagcttttctcggcttctggttcatcatat-atagtcttctccacaattattctgatgtttgtgtcgtggtttccaaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC
| | |||| | ||| | | | || | | | | | || || | | | | | |||| | |||| ||| || | ||| ||| | || ||||||||||| || |||||||| ||||| ||||| |||||||| || |||||||||||||| ||||| || |||||
gtaagttcccacaatctcttacctttgttgttgtggaaactgttggatttctttaaat-caagtacttgacaccactgtgttgttaata-ctgtactgac-taggtgttgtgtttctt---cttctagGTTGGCTTTCTGTGGTATGAATATATATACAAGCTAGACAAAGTTACATACAACAAGTACCATCCCTACACATCATGGATCCCTATAAC

upper sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G076394_T01 (Zea mays), 3'ss of exon 10
gtgagtt--gttagcttttctcggc--ttctggttcatcatatatagtcttctccacaattattctgatgtttgtgtcgtggtttccaaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC
|| |||| | | ||| ||| | | | || | || || | | | | | | | | || | || | |||| || || || ||||| ||||| ||||||||||||||||| ||| || ||||| || ||||||||||| || ||||||||||||||
gtaagttccatgatcttctcttgccagtgttgatgcactgactaggatgagtttaaggaaatgattaactacaattttctg---ttcattcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATATAACAAGTACCATCCCTACACGTCGTGGATTCCAATAAC

upper sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 11
---------------------------gtgagttgttagcttttctcggcttctggttcatcatatatagtcttct-------ccacaat---tattctgatgtttgtgtcgtggtttccaaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC
| | ||| || ||||| || || | | | ||| || | ||| ||| || | | | | | || | | ||| ||| ||| | |||||||||||||| ||||||||||||||||| | |||||||| || |||||||| |||||||||||||| ||
gtgagttacatctcttacaataagattattcatggttttctattctcctgttatgttattacttcaatattccttgatgtagaccaaaatgggtaaacaagaacatctctttttcatttttcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATACAACAAGCTCCACCCCTACACCTCTTGGATTCCAATTAC

upper sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 11
--------------------------------------------gtgagttgttagctt--ttctcggcttctggttcatcata-tatagtcttctccacaattattctg-atgtttgtgtcgtggtttccaaatgttc-agGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC
|| || || | || | | | | |||| || | | | | ||| ||| | | | | || | || | ||| ||| ||| ||| | |||||||||||||| ||||||||||| ||||| | |||||||| || |||||||| || ||||||||||| ||
gtgagttacatgtcttacaataagattatttgctaagattattcatggttttctattctccttttatgttattacttcaatattctttgatgtagaccaaaatgggtaaacaagaacatctcttttcatctttcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGATAAGGTCTCATACAACAAGCTCCACCCCTACACCTCATGGATTCCAATTAC

upper sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------gtgagttgttagcttttctcggcttctggt----tcatcatatatagtcttctccacaattattctgatgtttgtgtcgtggttt-ccaaatgttc---agGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC
|| | | | | | | || || | | || |||| | | | | || || | | || | | | || | | | || ||| |||||| | |||||||||||||| |||||||||||||| ||||| || || || | |||||||||||||| ||||||||||||||
gtaagttgcatgatcctgtgatcacagtattattcttatctgtttagattttaagtgacttttttatttatactttctttttcttttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC

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|125004487|gb|EL076756.1|EL076756
EST:     GGATGTCAATCAAGACAAGCATAANAGGAATTTCTTCATTC                         GCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTAC
genomic: GGATGTCAATCAAGACAAGCATAATAGGAATTTCTTCATTCgtgagttgtt ... aaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTAC
EST: gi|125233605|gb|EL247690.1|EL247690
EST:     TAGGAATTTCTTCATTC                         GCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTAC
genomic: TAGGAATTTCTTCATTCgtgagttgtt ... aaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagtcttctccacaattattctgatgtttgtgtcgtggtttccaaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC
                    ttctgat  putative branch site (score: 3)
 acaattatt  TA-rich tract