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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGTTGTCTGTTGGCTATACCTTGGATCAGATTCCTAATGATATCACGAGGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGgtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcag

Basic information

species Arabidopsis thaliana
transcript AT1G29900.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G29900.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os01g38970.1 (Oryza sativa), 5'ss of exon 1
CAAGTTGTCTGTTGGCTATACCTTGGATCAGATTCCTAATGATATCACGAGGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGgtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcag
 ||| | ||||| || ||||| ||||| |||||||| |||||||| |||| ||| || || |||||||| ||||| ||||| || || ||||| |||||||||||   || |   || ||    | |  | | ||| | ||||| ||  | |  ||| || |  | |     ||| | ||  | | ||  | || || ||    |||                                      
AAAGCTCTCTGTAGGTTATACTTTGGACCAGATTCCAAATGATATTACGAAGAAGACTCCTGCTAGCTTTGAGCCTTCCATTGACTACGTGGTCACTAAGgtttgctttttccctctgtt--tctaagatttcttgggcaatgatatttggtgcactgtgcaattgt---tgcatttttcatccttat--tttagaagctatcttgc--------------------------------------

upper sequence: AT1G29900.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G700683_T01 (Zea mays), 5'ss of exon 1
CAAGTTGTCTGTTGGCTATACCTTGGATCAGATTCCTAATGATATCACGAGGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGgt-ttgt--cattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttaca---cacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcag
 ||| | || || ||||| ||  | ||||||||||| |||||||| || | ||| || || |||||||||||||| ||||| ||||||||||| || ||||| || |  || ||  | || || ||||| ||  |  || |||   || |   | ||    |    || | ||   || || || |  ||  ||  |   |                                                  
GAAGCTCTCAGTAGGCTACACTCTAGATCAGATTCCCAATGATATTACCAAGAAGACTCCAGCTAGCTTCGAGCCTTCCATTGATTATGTGGTTACAAAGgtattattccaatctgt-ctcttagctttcttaattgtgtgaatgaagtttttcctgcaaatatgcatctgcagtacatatttaacttctctatattcctt--------------------------------------------------

upper sequence: AT1G29900.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G061990_T01 (Zea mays), 5'ss of exon 1
CAAGTTGTCTGTTGGCTATACCTTGGATCAGATTCCTAATGATATCACGAGGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGgt----ttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttaca-cacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcag
 ||| |||| || ||||| ||  |||| |||||||| |||||||| || | ||| || || |||||||||||||| ||||| ||||||||||| || |||||    ||   ||  ||   | |  ||||| || ||   || ||   || |      |    |    || | ||  | || | |  |||||    |||                                                    
AAAGCTGTCAGTAGGCTACACTCTGGACCAGATTCCCAATGATATTACCAAGAAGACTCCTGCTAGCTTCGAGCCTTCCATTGATTATGTGGTCACAAAGgtatcatttcaatctcagtttctcagctttcttagttgcgcaaatgaagttttttccgcaaatatgcatctgcagtatatat-tttacttctctgtattcc-------------------------------------------------

upper sequence: AT1G29900.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA15G05020.2 (Glycine max), 5'ss of exon 2
CAAGTTGTCTGTTGGCTATACCTTGGATCAGATTCCTAATGATATCACGAGGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGgtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttg-aagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcag
 ||||||||||| || ||| | ||||||||||| || || ||||| |||| ||| ||||||||||| || |||||||| || ||||||||||| ||||||||  |         |  || |   ||  |  | |||| |    | |      |||||| | | ||| |    || | ||     |  ||  | ||||      ||  |                                      
AAAGTTGTCTGTGGGGTATTCTTTGGATCAGATACCAAACGATATAACGAAGAAGACACCGGCTAGTTTTGAGCCCTCAATTGATTATGTGGTTACTAAGgtaagg--------agcttagttgttgctgatattgccatcatataccaatgtgacttggtaggatgtttttacttttaaattgtaaattttgtataggtaataagtc--------------------------------------

upper sequence: AT1G29900.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA13G40380.1 (Glycine max), 5'ss of exon 2
CAAGTTGTCTGTTGGCTATACCTTGGATCAGATTCCTAATGATATCACGAGGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGgtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcag
 ||||||||||| || ||| | |||||||| || || || ||||| |||| ||| ||||||||||| || |||||||| || ||||||||||| |||||||| ||  | |   |  | |||    ||||   | |  || ||   |      |||||| | ||  |       || | |  | |  |   | | || | |     | |  |                                  
GAAGTTGTCTGTGGGGTATTCTTTGGATCAAATACCAAACGATATAACGAAGAAGACACCGGCTAGTTTTGAGCCCTCTATTGATTATGTGGTTACTAAGgtatgcaacttagt--tgttgatgatatt---gctatgatatacca---atgtgacttggtaggatggttttaattt-taaattgtaaattttgtatagttg---gtaagtc---------------------------------

upper sequence: AT1G29900.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv06s0004g03360.t01 (Vitis vinifera), 5'ss of exon 1
CAAGTTGTCTGTTGGCTATACCTTGGATCAGATTCCTAATGATATCACGAGGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGg----tttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcag
      ||| ||||| ||  | |||||||||||||| ||||| ||||| | ||||||||||||||| || ||||| ||||| |||||||||||||| ||||    | | |   ||||| || |||   |  ||  |  ||| ||      |  | |     ||| ||  ||   ||  |  ||    ||||||  ||  |   || |                                          
------GTCGGTTGGTTACTCATTGGATCAGATTCCAAATGACATCACAAAGAAAACACCGGCTAGTTTTGAGCCTTCCATAGATTATGTGGTGACAAAGGCAAGTgtctttctccattctattgtactagttatttatgctaatgtttctttgttaattgttgtagtatttggcatttgaatat-tttcatgtcatcgatgttcta------------------------------------------

upper sequence: AT1G29900.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S343_21V6.1 (Physcomitrella patens), 5'ss of exon 4
CAAGTTGTCTGTTGGCTATACCTTGGATCAGATTCCTAATGATATCACGAGGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGgtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatg-catattttgcttaacgatatctatttctttaccatgcag
 ||  |||||||||| | |||  ||||||| ||||| |||||||||||||||||||| || || || ||||||||||| || ||||| || || ||||||||     ||||          |  || | ||   ||    ||  || ||  |   | ||    ||  ||    || |   ||       ||  ||| ||| |     |  |||| |  |     | | |     |||||       
GAAACTGTCTGTTGGATTTACACTGGATCAAATTCCAAATGATATCACGAGGAAAACTCCAGCCAGTTTCGAGCCCTCGATTGATTACGTTGTCACTAAGgtacagtattcatcttccaatgtgttttgtgacctgtttgattggagacattgttcatttttaatgcactaggatgtcatcatgctgaaatgaatacactaactcatcggatttcgtgtc----tttttggagttttacag-----

upper sequence: AT1G29900.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S43_32V6.1 (Physcomitrella patens), 5'ss of exon 4
CAAGTTGTCTGTTGGCTATACCTTGGATCAGATTCCTAATGATATCACGAGGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGgtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttacca-tgcag
 ||  | || || || || || |||||||| ||||| ||||||||||| | |||||| || ||||| || ||||||||||| || || || || ||||||||    | |||    |        || | ||  |||    ||         ||    |     ||||| | ||   |    |  | |||| ||   ||   | |  |||    |  |      | ||  | | |  |    | |||
AAAACTTTCAGTCGGATACACATTGGATCAAATTCCAAATGATATCACCAAGAAAACTCCAGCTAGTTTTGAGCCCTCCATTGACTACGTTGTTACTAAGgtgcagccttctcccccaaataagttctatgctttgtaggattcttggtattt---ctcatgtatttaaaaacgagttatta--tgatgaaatgggaagatagactcatcgcgtttt-----gtgtccgtctttggagtggtacag

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|125239799|gb|EL253884.1|EL253884
EST:     GGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAG                         ATTCCTCGATTTG
genomic: GGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGgtttgtcatt ... taccatgcagATTCCTCGATTTG