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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgtaagtccagattgtgtttttatgttagtttctcttcgttatcgagttactgtgatttgagttactgattgttgtttaatgcag

Basic information

species Arabidopsis thaliana
transcript AT5G57655.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57655.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 5
CATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgtaagtccagattgtgtttttatgtt-agtttctcttcgttatcgagttac-tgtgatttgagttactgattgttgtttaatgcag--------
||||| |||||||| |||||||| ||||| ||||||||  |||| |||| |||||||||||| ||||| || || ||  ||   ||||||||||||||||||| | | |     || ||| ||||| || |||  ||| ||||  | || |  ||    | | | |   | |  ||| | |             
CATACGTTCCGTGGTACTGGAGGAGATCCTTTTGGTGCCCCTACAAAGTCTTGGCCTTGGGAGGATGGCACAAATTCGTTGGACATGGCTAAGAGAAGAAgtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcag

upper sequence: AT5G57655.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G081682_T02 (Zea mays), 5'ss of exon 5
CATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgtaag-------tccagattgtgtttttatgttagtttc--tcttcgttatcgagttactgt-----gatttgagttactgattgttgtttaatgcag--------
|| || |||||||| ||||| | |||||| || |||||| |||| |||  |||||||||||| || || || || ||| || | ||||||||||||||||||| |        | |   |   ||| |    ||||  |   ||||    |   |||   ||       || ||   ||| | |  ||||| |    |        
CACACGTTCCGTGGTACTGGCGCTGATCCTTTCGGTGCTCCTACAAAGACTTGGCCTTGGGAGGACGGCACAAATTCTTTGGCCATGGCTAAGAGAAGAAgtatgatgattgcctaacctacctttgtgctgtagtcccagccttctgggttatgttttggtctgtttgttggaagaactaacttctgtttcaactggcattgcag

upper sequence: AT5G57655.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: AC190975.3_FGT004 (Zea mays), 5'ss of exon 2
CATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgta-----agtccagattgtgtttttatgttagtttctcttcgttatcgagttactgtgatttgagttactgattgttgtttaatgcag
|| || ||| |||| |||||   |||||| ||||||||| |||| |||  |||||||||||| ||||| || || ||  || | |||||||||||||||||||     |   |  |   |   ||| ||||    || |  | || | | ||||   || ||||   |  |  |   |    | |||||
CACACGTTCTGTGGTACTGGCACTGATCCTTTTGGTGCTCCTACAAAGACTTGGCCTTGGGAGGATGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgatgatcgcctaacctacctttgtgttgtagtcccagccttct-gggtta---tgttttggtctgtt--tcaattggcattgcag

upper sequence: AT5G57655.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 5
CATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgtaag-------tccagattgtgtttttatgttagtttc--tcttcgttatcgagttactgtgatttgagttactgattgttgtttaatgcag
|| || |||||||| ||||| | |||||| ||||||||  |||| |||  |||||||||||| || || || || ||  || | ||||||||||||||||||| |        | |   |   | | | |  ||||| |   ||||    |   |||  |  ||  | | ||     |   |   || |||||
CACACGTTCCGTGGTACTGGTGCTGATCCTTTTGGTGCGCCTACAAAGGTTTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggatcacctaacctaactctatgttgtagttccagccttctgggttatgtttgttggaactaacttctgtttcaatcactattgcag

upper sequence: AT5G57655.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 5'ss of exon 6
CATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgtaagtccagattgtgtttttatgttagtttctcttcgttatcgagttac-tgtgatttgagttactgattgt---tgtttaatgcag-----
|| || |||||||| || ||||||||||||||||||||  |||| |||| |||||| ||||||||||||||| | ||  || ||||||| ||||||||||||||||  |   | | || || |   | ||  |  | |||    | |    | | |  |||   |    ||     | || ||| ||      
CACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTACTGATTCATTGGCTATGGCCAAGAGAAGAAgtaagttgaatctatattgttcttccatttattaattgttggaaaatagtgtataacatgaccgatctttttcctctattaaatacaacttag

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|86055233|gb|DR350990.1|DR350990
EST:     TTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAA                         TGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGGTGTT
genomic: TTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgtaagtccag ... tttaatgcagTGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGGTGTT
EST: gi|164059866|gb|ES166275.1|ES166275
EST:     TTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAA                         TGAGAGCTAACTTTGAGTTCTTGAAGA
genomic: TTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgtaagtccag ... tttaatgcagTGAGAGCTAACTTTGAGTTCTTGAAGA
EST: gi|116424348|gb|EG466940.1|EG466940
EST:     TTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAA                         TGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGGTGTT
genomic: TTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgtaagtccag ... tttaatgcagTGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGGTGTT
EST: gi|301501388|gb|HO206928.1|HO206928
EST:     TTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAA                         TGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGGTGTT
genomic: TTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgtaagtccag ... tttaatgcagTGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGGTGTT
EST: gi|164067780|gb|ES116169.1|ES116169
EST:     TGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAAGAGAAGAA                         TGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGG
genomic: TGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCT-AAGAGAAGAAgtaagtccag ... tttaatgcagTGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTACTAACTCTGTGTCTATGGCTAAGAGAAGAAgtaagtccagattgtgtttttatgttagtttctcttcgttatcgagttactgtgatttgagttactgattgttgtttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA