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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAGgtgagtatcgaaatggccactatgttgcctccttctctcacctatgcccatgaatattttctgaagaacaaacttaaccaaatattctcatgttgactttgatctggggtgtag

Basic information

species Arabidopsis thaliana
transcript AT1G27320.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 5
TTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAGgtgagtatcgaaatggccactatgttgcctccttctctcacctatgcccatgaatattttctgaagaacaaacttaaccaaatattctcatgttgactttgatctggggtgtag
||| | || |||||||||||||| |||||||||||||||||||||||||||||| |||      |  |||    | |        |   |    || ||    | ||    |||    |||  ||||     |  |||   || |||  || |   ||        
TTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttagtcc----actgccttcgtttcaaaataattgttgttttaggctttggcatcaactct----aacttacttctatgagcattaatattttggtttcgccttgat------

upper sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G423456_T02 (Zea mays), 5'ss of exon 6
TTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAGgtgagtatcgaaatggccactatgttgcctccttctctcacctatgcccatgaatattttctgaagaacaaacttaaccaaatattctcatgttgactttgatctggggtgtag
||| | || |||||||| ||||| |||||||||||||||||||||||||||||||||  || |      |  ||   ||     |  ||| |  | |    || |   |     ||   |  |  ||   |  || ||                            
TTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGgtgaggttctagtccatc--taaactgtacaataatcttaattgt--taattagagtgaaaggagatatgatgtt--tccgattttgcag------------------------

upper sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G471529_T01 (Zea mays), 5'ss of exon 6
TTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAGgtgagtatcgaaatggccactatgttgcctccttctctcacctatgcccatgaatattttctgaagaacaaacttaaccaaatattctcatgttgactttgatctggggtgtag
||| | || |||||||| ||||| ||||||||||||||||||||||| |||||||||  || ||   |   |||  |||     |  | |   |  ||   || |         ||   |  ||  |  |||| | ||                            
TTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTCCTAGgtgaggttctaat--gtatctaaattgtacaataatttt--cattgttaattagggcgaaaggagatatgaatgtttccaatttttgcag------------------------

upper sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 6
TTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAGgtgagtatcgaaatggccactatgttgcctcct------tctctcacctatgcccatgaatattttctgaagaacaaa--cttaaccaa--atattctcatgttgactttgatctggggtgtag
|| ||||| |||||||| |||||||||||||| ||||||||||||||| |||||||||       || | |   | | | |   |      | | | |  | |  | ||  | |||     || || ||   |||   ||   ||   |      | | || ||| |   |     
TTTCTTGCTACTGTTTCCCATGAAATCAGAACACCAATGAATGGTGTTTTAGgtgagttgtcttctgtctatggtttagtcgattatccaatttttaatttttaactatatacattccacaaaaaagaagagcttcttcagccatgaccctgctctaaattggattttcag-----

upper sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G11060.2 (Glycine max), 5'ss of exon 7
TTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAGgtgagtatcgaaatggccactatgttgcctccttctctcacctatgcccatgaatattttct---gaagaacaaacttaaccaaatat--tctcatgttgactttgatctggggtgtag
|| ||||| |||||||| ||||| |||||||| ||||||||||||||| | |||||||       || | ||    | | ||  || ||  |  | |  | || | ||||| |     ||  |  | |||   ||   ||   |      | | || ||| |   |     
TTTCTTGCTACTGTTTCCCATGAGATCAGAACACCAATGAATGGTGTTTTGGgtgagttgtcttctgtctacggcttagtcta-ttatccaatttttatctat-attatttccacagaaaagaagagcttcttcagccatgaccctgctctaaattggattttcag-----

upper sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0010g03780.t01 (Vitis vinifera), 5'ss of exon 6
TTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAGgtgagtatcg--aaatggccactatgtt-gcctccttctctcacctatgcccatgaatattttctgaagaacaaacttaaccaaatattctcatgttgactttgatctgg-ggtgtag-----------------
||||||||||||||||| ||||| |||||||| ||||||||||||||||| ||||||| |    ||||     || | ||  | ||  ||        ||  |     |  |||  | |  || ||| |||    || | |   | | |      |   ||   || ||                  
TTCCTTGCCACTGTTTCTCATGAGATCAGAACCCCAATGAATGGTGTTCTCGgtgagttttcttaaatttatgctctattcacttcagtcatgtctagatatcgcctcacctttgatcagaaataaa-ttatgggaacactgaaaagattttggagccatgacagtctaaatatgttcatcttgcag

upper sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S50_141V6.1 (Physcomitrella patens), 5'ss of exon 7
TTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAGgtgagtatcgaaatggccactatgttgcctccttctctcacctatgcccatgaatattttctgaagaacaaacttaaccaaatattctcatgttgactttgatct--ggggtgtag
||| | || ||||| || || || ||  | |||||||||||||||||||||||| |||||  | ||  |||| |     | |   | ||  || | ||        |||||       |  | | ||   |  ||||| || || | |  |  ||||  | | || ||
TTCTTGGCAACTGTGTCTCACGAGATTCGGACTCCAATGAATGGTGTTCTAGgttagtat-aatatatccacaa---cacttgaatttcatactt-tgt-------tatttct----aagtagaattgtgcgcatattgtc-tgcttatgtacatctctgtgatgcag

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|125182831|gb|EL198050.1|EL198050
EST:     AATGGTGTTCTAG                         GAATGTTGCATATGCTTATGGACACAGAGTTAGATGTTACGCAACAGGATT
genomic: AATGGTGTTCTAGgtgagtatcg ... tggggtgtagGAATGTTGCATATGCTTATGGACACAGAGTTAGATGTTACGCAACAGGATT