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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttgtgcag

Basic information

species Arabidopsis thaliana
transcript AT1G50370.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 7
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaat----aaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttgtgcag------------------
 ||||||||||| ||||||||||| |||||||| || || ||||||||||| || || |||||||||||||||||||| || ||  | || ||  ||||||||| || | |  |||   |  ||   | |  | |    |  | |||   | |  | | |  |||   | ||    ||   | ||||   |     ||                     
TTTCTGTGATCTAATGTGGAGTGACCCTGAAGAAATAGAGACATGGGCTGTTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacag-tcactacattctggatcatctattaattgtttccttgtaaatgtttttcatctaccttttgcag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G518717_T03 (Zea mays), 5'ss of exon 3
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttgtgcag
 ||||| ||||||||||||||||| ||||| || || || ||||||||||| ||||| |||||||| |||||||| || || ||  | || ||  | |||||   ||||   |   ||    ||  | ||   || |    |||       |   | |||||  | | | || |   ||       ||  | |||||
TTTCTGCGATCTTATGTGGAGTGACCCTGAGGAGATAGAGACATGGGCTGTTAGTCCCCGTGGAGCAGGTTGGCTGTTTGGATCGCGAGTAACAGCAGAGgtgagtatacaat---ctataatttcattt---attatccttgat------tgtttttattt--gctacttg-tgaatgtcaccttttgctatgcag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G055905_T02 (Zea mays), 5'ss of exon 7
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttg---tgcag
 ||||| || |||||||||||||| ||||| || || || ||||||||||| ||||| |||||||| |||||||| || || ||  | || ||  | ||||| | |||    | |    || ||  | ||| | ||   ||            | ||| |||   ||| ||  |    | | |  | | |||   |||||
TTTCTGCGACCTTATGTGGAGTGACCCTGAGGAGATAGAGACATGGGCTGTTAGTCCCCGTGGAGCAGGTTGGCTGTTTGGATCGCGCGTCACAGCAGAGgtttgtatgcaatgt---aggctt--atttttattattatg-----------gattgtttttttattctctccttgtggatgtcaccttttgccatgcag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA20G23310.4 (Glycine max), 5'ss of exon 7
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttgtgcag
 ||||||||||| ||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||| || |||||||| ||  | |||||| |   |||| ||| |    |||   || ||||    | |             | | ||| | |   || | | |||  ||  ||| |  |||||
TTTCTGTGATCTAATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTCCCCGTGGAGCAGGTTGGCTTTTTGGATCCAGGGTCACTTCGGAGgtaatgtaatttatttgttaa-ttgcttttagaattgaatat-------------tatgttttaat---cttaccagtgcatt--cttttcatgcag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA10G43480.1 (Glycine max), 5'ss of exon 7
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttgtgcag
 ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || ||||| ||||||||||| || |||||||| ||  | |||||| |   |||| |||                  | |  ||     |||| | ||| | ||| | |   || | |  ||  ||  ||| |  | |||
TTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTCCCCGAGGAGCAGGTTGGCTTTTTGGATCCAGGGTCACTTCGGAGgtaatgtaatttattt-----------------gttaattgcttttagaattgaatatgttttaat---cttaccattgcatt--cttttcatacag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA10G43470.1 (Glycine max), 5'ss of exon 7
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttgtgcag
 ||||||||||| ||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||| || || ||||||||  | |||||| |   |||| |||     |||  ||||    | || | |||| |        | |  || | |   || | | |||  ||  ||| |  |||||
TTTCTGTGATCTAATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTCCCCGTGGAGCAGGTTGGCTTTTTGGATCGAGGGTTACTTCAGAGgtaatataatttattt-----gtt--aattgcttttagatttgaatat-------tatgctttaat---cttaccagtgcatt--cttttcatgcag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 7
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttgtgcag
 || |||||||| ||||||||||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||| || ||| |||| ||  |||||||| |   | || |     |  |||    ||||||   || |  ||    ||   || |||| |     |  ||     |  ||| || |  |||||
ATTTTGTGATCTGATGTGGAGTGATCCTGAAGATATCGAAACATGGGCAGTCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaattgt-----gaattgcttattgaattgagtattgaacattatgtgtgaatttta-----caaat-----gccttgttt-tcatgcag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 5'ss of exon 7
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttgtgcag
 |||||||||||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||| ||||||||||| || || ||||| ||  ||||||||     ||    |   ||  | |   |||  | |     ||       |  ||| | |||   |||  |                          
ATTCTGTGATCTTATGTGGAGTGATCCTGAAGACATTGAGACGTGGGCAGTCAGTCCACGTGGAGCAGGTTGGCTTTTTGGATCAAGGGTCACGTCTGAGgtagagtgatacaatctcggcttcgtcttttccagacttcatgtttgctgaggaattttttttctttctttacag----------------------

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 7
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataa--atgtatttcagttccctgatctgtggttttgcttcttgtgcag--------
 ||||||||  | ||||||||||||||||| ||||| ||||| |||||||| || ||||| || ||||| |||||||| ||  |  | |||||| |||||| |       |  | |||     |||| ||         |      || | ||   |||  ||  | || | ||   |   |||   |||   ||||          
ATTCTGTGACTTGATGTGGAGTGATCCTGAGGATATCGAAACTTGGGCTGTTAGCCCACGAGGTGCTGGGTGGCTTTTTGGTGCACGCGTTACCTCTGAGgca-------tgctctctaaacgtgaacttaattctgcctccagggaggagtagttatgagttggaatttcttggctttccgttgcactttgagtgctctatttaag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 5'ss of exon 7
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttc-agttccctgatc--tgtggttt---tgcttcttgtgcag----
 || |||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||| || ||||| ||||| |||||  |  | |||||| | |||| ||   |  ||  || |        |||||| |     | | |  ||||| |  | |||||  |  |   |  ||  ||   |||   |||| ||| |        
ATTTTGTGATCTGATGTGGAGTGACCCTGAGGATATCGAGACTTGGGCTGTTAGTCCACGAGGTGCTGGATGGCTCTTCGGTGCACGCGTTACCTCCGAGgcatgctttcttcattttaactc---aatttgcac----tctaaggagaaacagctttattttgaaatttattgtcaatgcactttaagtgctccttttaagcgaag

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|164173123|gb|EL974103.1|EL974103
EST:     TTTTCGGGTCCAGGGTTACCACTGAG                         TTTAACCATATTAACAATCTTGATCTAGTATGTCGCGCTCACCAGCTTGTA
genomic: TTTTCGGGTCCAGGGTTACCACTGAGgtatttatat ... tcttgtgcagTTTAACCATATTAACAATCTTGATCTAGTATGTCGCGCTCACCAGCTTGTA
EST: gi|164197037|gb|EL979586.1|EL979586
EST:     TCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAG                         TTTAACCATATTAACAATCTT
genomic: TCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatat ... tcttgtgcagTTTAACCATATTAACAATCTT
EST: gi|124793310|gb|EH882989.1|EH882989
EST:     TCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAG                         TTTAACCATAT
genomic: TCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatat ... tcttgtgcagTTTAACCATAT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTCCACGTGGAGCTGGTTGGCTTTTCGGGTCCAGGGTTACCACTGAGgtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT