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

gtgacttttgctttcaatcccttcaatataatacaaaccttttctctcttggtaatgaatcacttgaagaataatatcacattcttcatgacaatatttgaattttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT

Basic information

species Arabidopsis thaliana
transcript AT5G05580.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
gtgacttttgctttcaatcccttcaatataatacaaaccttttctctcttggtaatgaatcacttgaagaataatatcacattcttcatgacaatatttgaattttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT
        |    | |   |  |  || || | |      ||||  | | |  |  ||||   |     |   |    |         | ||| |||||  ||     ||  ||||||||||||||||| || |||||||||||||| |||||||||||||| ||||| || ||||| || 
-------gtaagatgagcgcgcttcatgtattcctggttctttcgttttggacag-gaattgttgttgaagctaaggaaggcagcatctcacattatttcgatccaattt-cagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG

upper sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G129209_T01 (Zea mays), 3'ss of exon 1
gtgacttttgctttcaatcccttcaatataatacaaaccttttctctcttggtaatgaatcacttgaagaataatatcacattcttcatgacaatatttgaattttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT
                                        |   |  |  |  | | ||   |  | |    |||          ||   | | ||||  |  ||    || ||| ||||||||||||| || |||||||||||||| || || || || || ||||| ||||||||||| 
---------------------------------------gtaattagcgagtcagttaaatgcaggcaatgcaatgcagtgcagctctatatattattgtatgttcaagtgcagGCGGATTAGCCACAGGACGCACCACCAGAACCACGGCCACGTGGACAAGGACGAGTCATGGCATCCC

upper sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G128971_T01 (Zea mays), 3'ss of exon 2
gtgacttttgctttcaatcccttcaatataatacaaaccttttctctcttggtaatgaatcact-tgaagaataatatcacattcttcatgacaatatttgaattttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT
                            ||  |  | || | | ||   || |  | | |  || |  || || ||    | ||  |  ||  | |   || | ||||     ||||||||||||||||| || ||||| || ||||| ||||| || ||||| ||||| || ||||| || 
---------------------------gtaggattacccatgtttcctatgctcgttagtttctgtcgaggatcat----cgttgatgttgtaagtgaatggaatttc-----agGAGGATTAGCCACAGGACGCACCATCAAAACCACGGTCACGTTGAGAAGGACGAGTCCTGGCACCCG

upper sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0067g01120.t01 (Vitis vinifera), 3'ss of exon 2
gtgacttttgctttcaatcccttcaatataatacaaaccttttctctcttggtaatgaatcacttgaagaataatatcacattcttcatgacaatatttgaattttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT
                      ||  || ||  |    ||   |||  | | |    | || | |||    || | |||  |   |  | |      || | | ||||    ||||||||||| || || || || || ||||||||||| ||||| |||||||| |||||||||||||| 
-----------------gtttgtccctaaaaccctgctctaccctcaatggttttacagtctcctgat---tattttcagctgaattgtaattgcgattcattattccc---agGAGGATTAGTCATAGGACCCATCATCAGAACCATGGACATGTTGAGAATGATGAATCATGGCATCCA

upper sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgacttttgctttcaatcccttcaatataatacaaaccttttctctcttggtaatgaatcac-ttgaagaataatatcacattcttcatgacaatatttga-attttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT
             | |    |||  |  |         | |    ||   | ||||||   || ||| |      |  || | |  | |  | | | |||||    ||    | ||| | ||||||||||| ||||||||||||||||| || || || ||||| ||||| ||||||||||||
------------gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT

upper sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
--gtgacttttgctttcaatcccttcaatataatacaaaccttttctctcttggtaatgaatcacttgaagaataatatcacattcttcatgacaatatttgaattttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT
  | || | || ||   |||  | ||  |    |   |     | || | |     |||   || | | ||| |  |  |  | | |   |||     |  |         || ||| |||||||||||||||||||||||||||||||||| ||||| ||||| ||||| || |||||||| 
gtgagaatctttctcataatgtcctccttcgtcttggagtagatgctgtttcacacatg--ccattggtagagttgtgactgaat-tgtgtgatggggtggg---------tgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG

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|124752210|gb|EH842340.1|EH842340
EST:     GTGGCTGGTCATCTTCTTCATTCCTCAATTCTGGTCCCTTACCATGGCTG                         GAGGATTAGCCACAGAACTCACCA
genomic: GTGGCTGGTCATCTTCTTCATTCCTCAATTCTGGTCCCTTACCATGGCTGgtgacttttg ... ttccttgtagGAGGATTAGCCACAGAACTCACCA
EST: gi|124863033|gb|EH947470.1|EH947470
EST:     CTTACCATGGCTG                         GAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGA
genomic: CTTACCATGGCTGgtgacttttg ... ttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttgaagaataatatcacattcttcatgacaatatttgaattttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT
                                           ttttccttgt  CT-rich tract
                               acaatatttgaatttt  TA-rich tract