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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttgattttgtgctaatgatttgcactggtgtgatagtgtgttgttttttgcgttctctttagttttctgttttctctcaatagtaacaaaag...

Basic information

species Arabidopsis thaliana
transcript AT4G16155.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgta-----aca-ttttgattttgtgctaatgatttgcactggtgtgatagtgtgttgttttttgcgttc-tctttagttttctgttttctctcaatagtaacaaaag
|||| | ||| | ||||| ||||||||||||||||| || || ||||| ||||| || || || || ||||||||||| |||||||| || ||||||||||||     ||| ||   |   ||    | |   |  |||  |  |   |    |   | ||||| || | |   |  | | |   | ||| |   | |         
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaaca-gacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt------

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 5
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttgattttgtgctaatgatttgcactggtgtgatagtgtgttgttttttgcgttctctttagttttctgttttctctcaatagtaacaaaag-----
|||| | ||| | ||||| || || |||||||| || || || |||||||| || || || ||||| ||||||||||| || || || ||||||||||||||| |||     || | ||||    ||     |  |  | || |  |   |  |  | |  |     | |  |  ||   |   |    || ||||         
TGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGATGTATATACAGCTCTTGGAAGTGAGgta-catgaaagttct-tgctgtgaataaattcaaggat-atggcttagagaatcatacagtgagcatggaatcatgcaattatt--gcagaaacatggttctac

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttgattttgtgct--aatgatttgc---actggtgtgatagtgtgttgttttttgcgttctctttagttttctgttttctctcaatagtaacaaaag
|||| ||||| | ||||| ||||| |||||||| || || || ||||||||||| || || ||||||||||||||||| ||||| || ||||||||||||||| ||||   |  |  ||||   || ||||||    ||| | |      |     || || ||     |          ||     |  | |   |   |    
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgta-cattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcccagtattcta----

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G145595_T02 (Zea mays), 5'ss of exon 4
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttgat--tttgtgcta--atgatttgcactggtg-tgatagtgtgttgttttttgcgttctctttagttttctgttttctctcaatagtaacaaaag
|||| | ||| | ||||| || ||||| |||||||| || || ||||||||||| || || ||||| ||||||||||| ||||| || || ||||||||||||        ||  ||   || |  ||   ||  |    || | |  | || |  |  | |  ||| | |||||       |  ||| |||    | |      
TGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGATGTATACACAGCTCTAGGAAGTGAGgtatatgaacaatcattcaagccatcattgcttaaatacatgcttagggagtctaatcgtgttagttat-tttagcgaatattcctctgtcatatatcatg----

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 5
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttgattttgtgctaatgatttgca--ctggtgtgatagtgtgttgtttttt----gcgttctctttagttttctg--ttttctctcaatagtaacaaaag------------------------------------------------------------------------------------
|||| | ||| ||||| | |||||||| ||||| || || ||||||||||||||||| || ||||| ||||||||||| || |||||||||||||||||||||  | ||   || ||   || |  |||  |  ||      || || | |||||  |     |   |  |  ||||||||    |||||| | |  |      ||||                                                                                    
TGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGATGTATATACGGCCCTTGGAAGTGAGgtagtacttctcttctgatatatttttttttatcctttctcaattgtattttgttcatgagaagaactgacaatagttttccaatttttcttttatgacgtttgaaagttttttatattatctcattgtttgaaaagttagaaacctaatttgtgcagaagagatatagttggtaataatggtactctgcag

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 5
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttgattttgtgctaatgatttgcactggtgtgatagtgtgttgttttttgcgt-tctctttagttttctgttttctctcaatagtaacaaaag--
 ||| | ||| ||||||| |||||||| ||||| || || ||||||||||| ||||| |||||||| ||||||||||| || || || ||||||||||||||| ||  |    |||||| || || ||    ||  | | ||    | ||||| ||      | | | ||  |    | |  ||     |   | || ||   
CGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGATGTATATACAGCACTTGGAAGTGAGgtagcacatc---tttgtgatactgtttctttcttttttcattaccttttgttcttgataaatatttataaataatcgatcccttcatttgacatcagaaata

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G37050.2 (Glycine max), 5'ss of exon 5
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgta--acattttgatt--ttgtgctaatgatttgcactggtgtgatagtgtgttgttttttgcgttctctttagttttctgttttctctcaatagtaacaaaag
 ||| | ||| |||| || |||||||| ||||| || || ||||||||||| ||||| |||||||| ||||||||||| || || || |||||||||||||||  |||| ||  |   || || || |  ||    ||  | | ||    | ||||| ||         ||     |  |   | || ||| | |  |      
CGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGATGTATATACAGCACTTGGAAGTGAGgtagcacatctttgtgaattttgatactttttctttctcttttcattaccttttgttcttgagaaatatttacaaataatcaatcctatcatttgacatc----

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttgattttgtgctaatgatttgcactggtgtgatagtgtgttgttttttgcgttctctttagttttctgttttctctcaatagtaacaaaag------------------
|||  ||||  ||||||   | || ||||||||||| || || ||||||||||| || |||||||||||||| ||||| || || ||||||||||||||||||| ||||     ||| ||  || |||  || |    | | |||| | ||| |   | |   | | || || ||||       |      | ||                       
TGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGATGTCTATACTGCCCTTGGAAGTGAGgtaaaattt---ccttgcgc--attattgacaataaaataaaagtg-gatgtgtggagtgcg-tgtgtaattatctgacaataattggagctgacttcccttttctgtgggcttgcag

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttgattttgtgctaatgatttgcactggtgtgatagtgtgttgttttttgcgttctctttagttttctgttttctctcaatagtaacaaaag----------------------
 || ||||| || ||||   |||| |||||||||||||| || || || ||||| || ||||| |||||||||||||| ||||| || || ||||| |||||  || |     |||||   |  |  | | |    | | ||  | |  | ||||||   ||     ||  | |   |    | |    | | ||||                         
CGCTTTGAAGTTAGAGTGGATTCCAGACTGGATTGCGATCGTTGGCAGCGGTTACATTGGTCTAGAGTTCAGTGATGTATACACAGCTCTCGGAAGCGAGgt--cagtaaccgtttgtctcacggtctaggagcatttttattttattctattttttcactttgtcgtatatcttcatcacttgtatggactcacaagttgacctcttttcgtgcccggcag

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttg----------attttgtgctaatgatttgcactggtgtgatagtgtgttgtttt------ttgcgttctcttt-agttttctgttttctctcaatag--taacaaaag
||| |||||  ||||||   |||| ||||||||  | || || ||||||||||| || |||||||||||||||||||||||||| ||||||||||| ||||||   ||||           |   | |  | |  | |   |  | | |  | |  | | |||||      |||   |||  |  || ||  | |  |||  |  | |  |  ||    
TGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGATGTTTACACTGCCCTTGGAAGCGAGgtacagttttattgaaaggacacaatatttttaaaaataaaatggatatattgggttctagttttaaaaagttgtcatctagtggagcttattttcctcttgctgtgggttggcag---

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|125047642|gb|EL119911.1|EL119911
EST:     TTATATCGGTCTTGAGTTCAGTGTATGTTTACACGGCCCTTGGAAGTGAG                         GTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTG
genomic: TTATATCGGTCTTGAGTTCAGTG-ATGTTTACACGGCCCTTGGAAGTGAGgtaacatttt ... ttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTG
EST: gi|124873042|gb|EH954687.1|EH954687
EST:     CCCTTGGAAGTGAG                         GTAACTTTTACTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAG
genomic: CCCTTGGAAGTGAGgtaacatttt ... ttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttgattttgtgctaatgatttgcactggtgtgatagtgtgttgttttttgcgttctctttagttttctgttttctctcaatagtaacaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgttctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa