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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgtcacttacctactatttcccctattaggttgtgtgaatattgtaatgttttgataatctgttgttttatttgttgtag

Basic information

species Arabidopsis thaliana
transcript AT3G06400.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 14
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgtcacttacctactatttcccctattaggttgtgtgaatattgtaatgttttgataatctgttgttttatttg---ttgtag----------
|||||  | ||||| || || |||||||| ||||||||  |||||||||| || |||||||| |||||||||||||||||  |||| |||||||||||||||| |    || ||  |   || | || |     |  |       | | |    | | |   |   |   | ||   |      |  ||           
ATTGACCGCATCATCGCTAAGGGAGAAGAAGCAACAGCACAACTTGATGCAAAAATGAAGAAGTTCACAGAAGATGCTATTAAGTTCAAAATGGATGACAgtatgaccctctctctctctctctctctctctcaatatctctcacacacttccttctctatgtctgcatatattcagtacaaactcataaagtttggtct

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: 13113.m00246 (Oryza sativa), 5'ss of exon 14
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgtcacttacctactatttcccctattaggttgtgtgaatattgtaatgttttgataatctgttgttttatttgttgtag
|||||  | ||||| || |||||||| ||  |||||||||| |||||||| || ||||| || |||||||| ||||||||  | ||||||||||||||||||| |       ||  |  | | | |  | |  ||        |  ||   || | |||| ||                        
ATTGACCGTATCATAGCTAAAGGAGAGGAAACAACAGCTGAGCTTGATGCAAAAATGAAAAAGTTCACAGAGGATGCTATTAAATTTAAAATGGATGACAgtatgtacccttctcccgcagtctctttctttctatcactcaggtctaacttagtctttttatgcag--------------------

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgt-cacttacctactatttcccctattaggttgtgtgaatat-tgtaatgttttgataatctgttgttttatttgttgtag---
|||||  | || || || |||||||| ||| ||||||||||||||||||| || ||||| || |||||||| || || ||  | ||||| |||||||| |||| |    | | |     |  ||| ||  ||       | ||    ||| | | |||||||  ||         |||||||  ||  |   
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgttcttatgtcttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgtcacttac-ctactatttcc-----cctattaggt-tgtgtgaatattgtaatgttttga-taatctgttgttttatttgttgtag
|||||  | || || || |||||||| ||| ||||||| ||||||||||| || ||||| || ||||| || ||||| ||  | ||||| |||||||| |||| |    |   ||    | |||||||      | ||||   | | | ||  | || |     | |   |||    || | || | || || ||
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgttttctgtttctatttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 14
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgtcacttacctactatttc---ccctattaggttgtgtgaatattgtaatgttttga---taatctgttgttttatttgttgtag---------
||||| ||||| ||||| ||||||||||| ||||||||||| ||||||||||||||||| ||||| || |||||||||||  | ||||| ||||||||||||| |  |  |  |||  ||  | |||   |  |  ||  ||  ||     |  |   |||   |   || | |||||||| | ||  ||||          
ATTGACAGAATTATTGCTAAAGGAGAAGAAGCAACAGCTGAGCTTGATGCTAAGATGAAAAAATTTACTGAAGATGCTATCAAATTTAAGATGGATGACAgtatg--taacctttaaatataaattctggctttgctaaatttggtttgattgatgtcgttagaaatctattttgttgtttaaattcctgtatacccataag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 14
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgtcacttacctactatttc---ccctattaggttgtgtgaatattgtaatgttttga---taatctgttgttttatttgttgtag---------
||||| ||||| ||||| |||||||| || ||||||||||| ||||||||||||||||| ||||| || |||||||||||  | ||||| ||||||||||||| |  |  |  ||   ||  |||||   |  |  ||   |  ||     |  | |||||   |   || | |||||||| | ||  ||||          
ATTGACAGAATTATTGCTAAAGGAGAGGAAGCAACAGCTGAGCTTGATGCTAAGATGAAAAAATTTACTGAAGATGCTATCAAATTTAAGATGGATGACAgtatg--taacctttgaatataatttctggctttgctaaagttggtttgattgatgatgttaaaaatctattttgttgtttaaatttctgtatatccacaag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 14
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaaggg--tgtcacttacctactatttcccctattag---gttgtgtgaatattgtaatgttttgataatctgttgttt-tatttgttgtag--------------------
||||||||||| ||||| |||||||| |||||||| ||||| || ||||| |||||||||||||| || |||||||| ||  | ||||| ||||||||||||| | |  | | | |       ||    |  |||| |   | | | |  |  || ||   |||      ||||| |||| || ||  |                        
ATTGATAGAATTATTGCTAAAGGAGAGGAGGCAACTGCTGAGCTAGATGCCAAGATGAAGAAATTTACTGAAGATGCCATCAAATTTAAGATGGATGACAgtatgtgcctataattctagctttaaaaacaatattggcatgatctttacaagttttatgctttcttctgtctgtagtttatagttactaatactggtgctttctttttgtag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 14
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgt-cacttacctactatttcccctattaggttgtgtgaatattgt--aatgttttgataatctgttgt-tttatttgttgtag----------------------------
||||||||||| ||||| |||||||| |||||||| || || |||||||| || ||||||||||| || |||||||| ||  | ||||| ||||||||||||| |    |     |||||  | |  |    |  |   | |  | ||  | |  |    ||| ||  | | || | ||| |   ||  ||                            
ATTGATAGAATTATTGCTAAAGGAGAGGAGGCAACTGCCGAGCTTGATGCCAAAATGAAGAAATTTACTGAAGATGCCATCAAATTTAAGATGGATGACAgtatgtacctatgactacctgttctagctttaaaaacaatattggcatgctctttacaagttttatgctttcttctgtttgtagtttagagttactaatactgatactttcttttgtag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 14
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgtcacttacctactatttcccctattaggttgtgtgaatattgt--aatgttttga---taatctgttgttt--tatttgttgtag---------
|| || || |||||||| ||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||  | |||||||||||||| |||| | |  ||   || | |    |  | ||  |   ||   |   || | |  || ||| ||    |||  | |  |||   |||| |  |           
ATAGACAGGATCATTGCTAAAGGAGAAGAGGCAACAGCTGAGCTTGATGCTAAGATGAAGAAATTTACAGAAGATGCCATCAAATTTAAAATGGATGATAgtatgtggatccactatccagggctctcactcattatttacttatctacttttgaaagttatggggctaaaatataatttaacatttatcctgctttgttcag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaaggg-tgtcacttacctactatttcccctattaggttgtgtgaatattgtaatgttttgataatctgttgttttatttgttgtag
|||||| | |||||||| ||||||||||| || || |||||||||||||| |||||||||||||| || || || || ||  | ||||| ||||| |||||||||   |    | |   |  | ||  || |||   |   |  |  ||                                       
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgcgtttttg-tgttctccttatctagcgtttcgtttaacag-----------------------------------

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: EFJ32950 (Selaginella moellendorffii), 5'ss of exon 13
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgtcacttacctactatttcccctattaggttgtgtgaatattgtaatgttttgataatctgttgttttatttgttgtag
|| ||| | || ||||| || |||||||  ||||| |||||||| ||||| ||||||||||| ||||| || ||||| || |||||||| ||||||||  ||||| |   | ||||   |    | ||   |     |  | || || ||  |                                  
ATAGATCGTATAATTGCGAAGGGAGAAGCTGCAACTGCTGAACTGGATGCAAAGATGAAGAAGTTCACGGAGGATGCGATTCAGTTTAAGATGGATGATCgtaagtgca-ctcttattaatccatcccatcacactatgttttgtattttacag---------------------------------

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|116473628|gb|EG516220.1|EG516220
EST:     TAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACA                         GTGCTGACTTCTATGATTTTGATGATGACAATAAG
genomic: TAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgt ... tttgttgtagGTGCTGACTTCTATGATTTTGATGATGACAATAAG
EST: gi|116473629|gb|EG516221.1|EG516221
EST:     TAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACA                         GTGCTGACTTCTATGATTTTGATGATGACAATAAG
genomic: TAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgt ... tttgttgtagGTGCTGACTTCTATGATTTTGATGATGACAATAAG
EST: gi|125316236|gb|EL330321.1|EL330321
EST:     AGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACA                         GTGCTGACTTCTA
genomic: AGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgt ... tttgttgtagGTGCTGACTTCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgtcacttacctactatttcccctattaggttgtgtgaatattgtaatgttttgataatctgttgttttatttgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG