Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttagcttttctcggcttctggttcatcatatatagtcttctccacaattattctgatgtttgtgtcgtggtttccaaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC

Basic information

species Arabidopsis thaliana
transcript AT1G29890.2
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