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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatagtgaatacttttgaaatcttgaaaggttttctctttatatgttcttaccattgtttaagtgatcattattgtcatctctttttctgatcgttatcatcgttttaccagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG

Basic information

species Arabidopsis thaliana
transcript AT4G21160.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g10480.1 (Oryza sativa), 3'ss of exon 7
----------------gtaattatagtgaatacttttgaa-atcttgaaaggttttctctttatatgttcttaccat----tgtttaagtgatcattattgtcatctctttttctgatcgttatcatcgttttac------cagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG
                 ||||| |  |||    || ||   | ||         |    || ||   ||  |||||     | | | | | |  |        |  |||| |||| |   | | |||   ||  |      ||||| || ||| |  | ||  | ||   |||| | |||||||||||||| || ||||||| |||||||||||||||  | || ||| |  | ||| ||
gtagtattatgaaatcctaattttc-tgatggtttctgggcaactaattcaagatcgaattcatcgttttgtaccacattgtctctcattcagaacatgcagaaattcttgttctaaatttcaccatatcttcgctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG

upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 5
-----------gtaattatagtgaatacttttgaaatcttgaaaggttttctctttatatgttcttaccattgtttaagtgatcattattgtcatctctttttctgat----cgttatcatcgttttaccagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG
             | || |  | |  |  | |    |   ||||  ||| | |||||| | || ||   | |     |||  |   | |||  |  | | |||||||     | ||       |    |||||  | |||  | |||||| | ||||| || || || || ||||||||||||||||| ||||| |||||||||||  | | |||   | |||| |||
gttggttgttctcacttctcattagcatatatattcttgggaaacttttgccctttatcttttatttttaattgaagagtagtagattttgataattttctttctgaattgactttggtgctatgcctccagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG

upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 5
-----------gtaattatagtgaatacttttgaaatcttgaaaggtttt--ctctttatatgttcttaccattgtttaagtgatcattattgtcatctctttttctga-tcgttatcatcgttttac-----cagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG
             | || |  | |  |    | || || ||  |   |||  |||||||| | || ||   | |     |||  |   | |||  |  | | ||||||| | |   |    | | ||      ||||  | |||  | |||||| | ||||| || || || || ||||||||||||||||| ||||| |||||||||||  | | |||   | |||| |||
gttggttgttctcagttctcattagcataaattaattcatgggaaacttttgctctttatcttttatttttaattgaagagtagtagatgttgataattttctttctgaattgactttggtgctatatgccttcagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG

upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 7
gtaattatagtgaatacttttgaa--atcttgaaaggttttctctttatatgttcttaccattgttt--aagtgatcattattgtcatctctttttctga-------tcgttatcatcgttttac-----cagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG
         ||   ||    | ||  ||||||  |   | |  || | ||| ||||    || |||   || | |  |  | |   |  | | |||||||       | | |   || | || |      ||||  |  ||  | ||| || | | ||||||||| || || |||||||||||||||  |||||| ||||||||| |  | |||||     | ||||||
---------gttggtatcactaaatgatcttgggaaactgttgctctgtatcttctatttatagttgtaaaatcagaaacagtaataattttctttctgaaattgatttggtgctattgcttaatgcctgcagACTGTCCAGACAACTATAATAAGGAGCAACTTGAATCCAGTCTGGAATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTG

upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 7
gtaattatagtgaatacttttgaaatcttgaaaggttttctctttatatgttc--ttaccattgtttaagtgatcattattgtcatctctttttctgatcgttatc-atcgtt-ttaccagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG
                         ||| ||   | |||   |  |  || |   || |  ||  |||     | || ||| |  |  ||  |  |||   ||  |  | | | |||| |||  |  ||  |    ||| | | ||||||||| || || ||||||||||||||||||||||| ||||| ||     | |||||  |  | ||| ||
--------------------cattgtctagattagattttagtcaaagtggtgaattgcttttagttagacagtgatcattctt-ttactgataatgaagattggctgttgctgttactagACTGTCCAGACACAGGTAATAACGAGCAACTTGAATCCAGTCTGGAATGAGGAACTCATGCTTTCTGTGCCCATGGATTATGGGCCCATAAAAGTG

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|86075296|gb|DR371053.1|DR371053
EST:     GAGATATGATGTCAAGTGATCCCTATGTTGTGTTGACTCTAGGACAACAG                         AAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAG
genomic: GAGATATGATGTCAAGTGATCCCTATGTTGTGTTGACTCTAGGACAACAGgtaattatag ... gttttaccagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAG
EST: gi|164036432|gb|ES151187.1|ES151187
EST:     CTCTAGGACAACAG                         AAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAG
genomic: CTCTAGGACAACAGgtaattatag ... gttttaccagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaagtgatcattattgtcatctctttttctgatcgttatcatcgttttaccagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG
                            ttctgat  putative branch site (score: 3)
                                           tcgtttt  putative PPT
        atcattatt  TA-rich tract