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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGGAGATCTCCAAAAGCAATGTCGTGGACGATATGGTTGCTAGCAATGGTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttgtgtgtttgttttgtag

Basic information

species Arabidopsis thaliana
transcript AT4G39800.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 7
TAAGGAGATCTCCAAAAGCAATGTCGTGGACGATATGGTTGCTAGCAATGGTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaatagagaaccggacagacactcaaaacctgt-ttctgttggc----aatctgagatcccattgat-ccaatttgtgtgtttgttttgtag
 |||||||||||||| |||||||| || || || |||||  | |||||||  ||||||| ||||| ||| || || || || ||||||||||| ||||||||    |      |          ||   | | || | |  ||       ||  |    |   ||| |  |   |   ||| ||  || || ||
CAAGGAGATCTCCAAGAGCAATGTGGTCGATGACATGGTCTCAAGCAATGCCATCCTCTATGAGCTTGGCGAGCATCCTGATCATGTTGTTGTGATCAAGgtttgcaatttgtccatggattcttctgcagcagtatgccattaaaaaaaaacttagttttggattaaaacttgtccatgtattc-ttctgcag

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G155242_T01 (Zea mays), 5'ss of exon 7
TAAGGAGATCTCCAAAAGCAATGTCGTGGACGATATGGTTGCTAGCAATGGTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaat-agagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttgt-gtgtttgttttgtag
 |||||||||||||| ||||| || ||||| || |||||  | |||||||  ||||||| |||||| || || || || || ||||| ||||||||||||||   | ||   | |   ||     | ||||   |||    |  ||||       |  ||||||   || ||||     || | ||| ||
CAAGGAGATCTCCAAGAGCAACGTGGTGGATGACATGGTCTCGAGCAATGCCATCCTCTATGAGCCCGGCGAGCATCCCGATCATGTCGTTGTCATCAAGgtctgttagctgatctttcacctcgttaaaa---gttgacatatgcaaggcagatttacattga---aacttgtcactcttttgttgcag

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 7
TAAGGAGATCTCCAAAAGCAATGTCGTGGACGATATGGTTGCTAGCAATGGTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaat-agagaaccggacaga-cactcaaaacctgtttctgttggcaatctgagatcccattgat-ccaatttgtgtgtttgttttgtag-------
 |||||||||||||| ||||| || ||||| || |||||  | |||||||  || |||| || ||| || || || || || ||||||||||||||||||||   | ||   | |   ||   |  | |||| |||   |     ||| | | |      ||| |     |    ||    |  ||||  |       
CAAGGAGATCTCCAAGAGCAACGTGGTGGATGACATGGTCTCAAGCAATGCCATTCTCTATGGGCCCGGCGAGCATCCCGATCATGTTGTTGTCATCAAGgtctgttagctgatcttccacctctttaaaaagctggcacgtgcagcagtttaaacgtagatttacattgaaacctgccactcctttgctgcatgcag

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA08G14670.3 (Glycine max), 5'ss of exon 6
TAAGGAGATCTCCAAAAGCAATGTCGTGGACGATATGGTTGCTAGCAATGGTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaatag-agaaccggacagacactcaaaacctgtttctgttggcaatctgag-atcccattgatccaatttgtgtgtttgttttgtag
 ||||| || ||||| |||||||| || |||||||||||    ||||| |  ||||||| ||||||||| ||||| ||||||||||| |||||||| ||||||| |   |      | ||  |||||     |   |||  ||||   | |      | | | | |  ||||  | | || |||||| ||
GAAGGAAATTTCCAAGAGCAATGTTGTTGACGATATGGTCAACAGCAACGCCATCCTCTATGAGCCTGGTGAACATCCGGACCATGTGGTTGTCATTAAGgtaatttttatttttagtcactcactctctttcaaattcaattggttctttatttgactcttcggt--aattaatttattggttttgcag

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA18G02210.4 (Glycine max), 5'ss of exon 7
TAAGGAGATCTCCAAAAGCAATGTCGTGGACGATATGGTTGCTAGCAATGGTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttg-tgtgtttgttttgtag
 ||||| |||||||| ||||| || || |||||||||||    |||||||  ||||||| ||||||||| ||||| || |||||||||||||| || |||||| ||      |    |      |||  |  | ||||| ||| ||      | ||   ||||| | || || | ||||   |||| ||
CAAGGAAATCTCCAAGAGCAACGTTGTTGACGATATGGTCAACAGCAATGCCATCCTCTATGAGCCTGGTGAACATCCCGACCATGTTGTTGTTATTAAGgtatatttgtttc--acccatttttcactatttctttctcttgtca------ggtct--ttgattctatctgctttgttgcctttgcag

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA18G02210.3 (Glycine max), 5'ss of exon 7
--------------------------------TAAGGAGATCTCCAAAAGCAATGTCGTGGACGATATGGTTGCTAGCAATGGTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttgtgtgtttgttttgtag
                                 ||||| |||||||| ||||| || || |||||||||||    |||||||  ||||||| ||||||||| ||||| || |||||||||||||| || |||||| ||      |    |      |||  |  | ||||| ||| ||                                          
ATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACGTTGTTGACGATATGGTCAACAGCAATGCCATCCTCTATGAGCCTGgtgaacatcccgaccatgttgttgttattaaggtatatttgtttc--acccatttttcactatttctttctcttgtcag-----------------------------------------

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA05G31450.4 (Glycine max), 5'ss of exon 4
TAAGGAGATCTCCAAAAGCAATGTCGTGGACGATATGGTTGCTAGCAATGGTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaatag----agaaccggacagacactcaaaacctgtttctgttgg--caatctgagatcccattgatccaatttgtgtgtttgttttgtag
|||||| |||||||| |||||||| || |||||||||||    ||||| |  ||||||| |||||| || ||||| || |||||||| |||||||| ||||||| |      |       |     | |||  ||    |  |       ||||  |  ||    ||||  |  || || | ||  ||||| ||
TAAGGAAATCTCCAAGAGCAATGTTGTTGACGATATGGTCAACAGCAACGCCATCCTCTATGAGCCCGGTGAACATCCAGACCATGTGGTTGTCATTAAGgtaattttttttatttttttatttttagtcactactccctctttcaaattcaattggttatttttttgacact-ttggtttattgtttttgcag

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 5'ss of exon 7
TAAGGAGATCTCCAAAAGCAATGTCGTGGACGATATGGTTGCTAGCAATGGTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaatag-agaaccggac----------agacactcaaaacctgtttctg--ttggcaatctgagatcccattgatccaatttgtg------tgtttgttttgtag
 |||||||||||||| |||||||| || ||||| |||||||| ||||| | |||||| | |||||||||||| ||||| |||||||| || |||||||||||| || | ||||||   |          |   | |  ||  | | | |||  ||||     |    || || ||    |  || |       ||||  | ||| ||
CAAGGAGATCTCCAAGAGCAATGTTGTCGACGACATGGTTGCCAGCAACGCTATCCTGTATGAGCCTGGGGAGCACCCTGACCATGTGGTGGTCATCAAGgtatatcgcagaaccctccttttgtttgtatgtattacaattcagatgctggtttggactcattcattctcactggctaacattatacggtgttgttgatattgcag

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 5'ss of exon 6
TAAGGAGATCTCCAAAAGCAATGTCGTGGACGATATGGTTGCTAGCAATGGTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccatt----gatccaatttgtgtgtttgttttgtag---------------------------------------------
 |||||||||||||| |||||||| |||||||| ||||| |||||||||   || || |  | ||| || ||||| || ||||| ||| |||| |||||||||     |   |    |   | |    |  |  | | |    || || |  | |   |||      ||||| |||| ||  |                                                      
CAAGGAGATCTCCAAGAGCAATGTAGTGGACGACATGGTGGCTAGCAATTCGATTCTATACGCGCCCGGTGAACATCCCGACCACGTTATTGTGATCAAGgtattcttatctctactccagc-cctgcagtcaatgttttcaagccatttcggctttgatttcagactccaagttgtctgcattcacaccgattctcgaatcttcctcttaaccaaaatcaatgacggcgtctgcag

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|86074513|gb|DR370270.1|DR370270
EST:     TATCCTCTTTGAGCCT-GGGAACACCCGGACCATGTTTGTTGTCATCAAG                         TATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCA
genomic: TATCCTCTTTGAGCCTGGGGAACACCCGGACCATG-TTGTTGTCATCAAGgtaaatagag ... tgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCA
EST: gi|47829945|gb|CK119629.1|CK119629
EST:     GTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAG                         TATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCA
genomic: GTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaatagag ... tgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCA