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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaatttctattccaaaaagtatctatatcctggtcaacgtttttcttcctctcaaggctgtcaaatatttttgtag

Basic information

species Arabidopsis thaliana
transcript AT1G09210.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaatttctattccaaaaagtatctatatcctggtca---acgtttttcttcctctcaaggctgtcaaatatttttgtag--
|||||||||||||||||||| |||||||||||||||||||| ||||| || || ||||||||||||| |||   ||||||||  ||||| ||  ||| ||| ||     | | |  |  |       ||    | | |||||   |    |      ||  | | ||| |    
CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtg--aatatctgtttactgatgcagatgcacttgaaacacttgcatatttctggtttctgacataaacatgtttctttttccag

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g61670.1 (Oryza sativa), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtt----tgtcaatttctattccaaaaagtatctatatcctgg--tcaacgtttttcttcctctcaaggctgtcaaatatttttgtag----
|||||||||||||||||||| |||||||| || ||||| || ||||| || || ||||||||||||| |||   |||||| |  |||||     ||| | |   || | ||   | | |  | |  || |  ||| | |     || ||| | |        ||  ||| |||      
CCTGAGGACTGGGATGATGAGGAAGATGGAGAATGGACAGCTCCAACCATTCCAAACCCTGAGTACAAGGGACCATGGAACCAAAAGgtatgagtgtgactgaatagttcatttactctagacaagctaggttcagcatcacgattactcactaattgcatgaaattttgtgtgtttag

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaatttctattccaaaaagtatctatatcctggtcaacgtttttcttcctctcaaggctgtcaa-atatttttgtag----
||||||||||||||||| || ||||||||||| ||||||||||| || || |||||||| || ||||  ||   |||||| |  ||||| || || || ||      ||  ||||  | |      ||||     ||| |  ||| |   ||| ||  || |||   | |    
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagttcct----tgaactgtatacaaactgacatcaa-----ttcatattctgatatctgacagcatgtttcacttgccag

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaatttctattccaaaaagtatctatatcctggtcaacgtttttcttcctctcaaggctgtcaaatatttttgtag
|||||||||||||| ||||| ||||||||||| ||||||||||| || || |||||||| || |||| |||   |||||| |  ||||| || || || || ||     |   |   | | |    |  |  || |  |  ||  ||    |||    |   ||   ||
CCTGAGGACTGGGACGATGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAGGGACCATGGAAACAAAAGgtatggcagttccttttaacctataaactgacagc--aattcatattctgatatctgacagca-tgttgtttcacttgccag

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA10G28890.1 (Glycine max), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtc--aatttctattccaaaaagtatctatatcctggtcaacgtttttcttcctctcaaggctgtcaaatatttttgtag-----------------------
||||| || ||||||||||| |||||||||||||||||  |||| || ||  ||||||||||||||| |||   ||||||| |  ||||||||   ||||| ||||  |||       ||| |      | || | || | |  | |   ||   | || |   ||| ||                        
CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGAGTACAAGGGCCCATGGAAGGCAGAGgtttgtggaaatttttattgtaaatttgtaatatttgaaatacgacatattccattatgttt-ggtaatgaatttgctttctaactttgcatgctacatatttgcag

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaatttctattccaaaaagtatctatatcctggtca--acgtttttcttcctctcaaggctgtcaaatatttttgtag-----------------------
||||| || ||||||||||| |||||||||||||||||  |||| || ||  |||||||||| |||| |||   ||||||| | |||||||||  |  | | ||    ||| |    ||||       |  || | || | |  | |   |  ||  || |   ||| ||                        
CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaaatttgttttgtaaatttgtaatatatgaaatatgacatattccattatgtttggaatg--aatttgctttataactttgcatgctacatatttgcag

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtca---atttctattccaaa---aagtatcta--tatcctggtcaacgtttttcttcctctcaaggctgtcaaatatttttgtag
||||| || ||||||||||| ||||||||||| ||||| || ||||| ||  ||||||| ||||||| |||   ||||||||| |||||||||       || || |  ||    ||  || ||  | | ||||| || |  ||      ||  ||  |      || | || | ||
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttttagtttaagttgaaacatttaattttgctggtaaaagagtt-----gtcataattcctctctatctcttggcag

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtc--aatttctatt--ccaaaaagtatctatatcctggtcaacgtttttcttcctctcaaggctgtcaaatatttttgtag
||||| || ||||||||||| ||||||||||| |||||  | ||||||||  | ||||||||||||| |||   ||||||||| |||||| |    ||| | ||||    || | |    |||    |  |  | |||     | | || ||   |     |    || | ||
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACACCTCCAACAATAGCTAACCCTGAGTACAAGGGACCATGGAAGCCCAAGgttcgctgaaatgtttattagttaagatgatgttatggaattttggaagttgacggttcacttaattgttcttgaaccattggcag

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|125260175|gb|EL274260.1|EL274260
EST:     CAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAG                         CAAATCAAGAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGAT
genomic: CAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaat ... atttttgtagCAAATCAAGAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGAC
EST: gi|116393133|gb|EG435725.1|EG435725
EST:     CTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAG                         CAAATCAAGAACCCCGACTACAATGGCAAGTGGGAGGCTCCATTGATTGAC
genomic: CTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaat ... atttttgtagCAAATCAAGAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGAC
EST: gi|116412926|gb|EG455518.1|EG455518
EST:     CTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAG                         CAAATCAAGAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGAC
genomic: CTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaat ... atttttgtagCAAATCAAGAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGAC
EST: gi|124886074|gb|EH964976.1|EH964976
EST:     CTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAG                         CAAATCAAGAACCCCAA
genomic: CTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaat ... atttttgtagCAAATCAAGAACCCCAA
EST: gi|116412928|gb|EG455520.1|EG455520
EST:     CTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAG                         CAAATCAAGAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGAC
genomic: CTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaat ... atttttgtagCAAATCAAGAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaatttctattccaaaaagtatctatatcctggtcaacgtttttcttcctctcaaggctgtcaaatatttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG