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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaagcaacttcttatcttttacattatagtcaatcttttcatggtcctaagatgatggcttcttgataccgtatctcctgatgaaattcttgcaaccctttgaagtataatgaccaattaatccaatgtgctggtatgccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACTTTACGAGCTGAGGAGGTATATTACTAGGCTGCACCTTGTATTTTTCTTA

Basic information

species Arabidopsis thaliana
transcript AT5G06600.3
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 16
----gtaacaagcaacttcttatcttttacattatagtcaatcttttcatggtcctaagatgatggcttcttgataccgtatctcctgatgaaattcttgcaaccctttgaagtataatgaccaattaatccaatg-tgctggtatgccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACTTTACGAGCTGAGGAGGTATATTACTAGGCTGCACCTTGTATTTTTCTTA
    ||     |    |    |   ||| |   ||      || |  | |  | ||||    ||    |     | | | |  ||    | |||||  ||  |   |||    || | |   || ||  |   ||| |     |||    ||||||| || ||| |   ||| |  || ||||| |||||||| ||||||||||| |||||||||||||||                                  
gttcgtgcatggtttatctgaagtatttcctgcatgaaaggtcctggcttt-ttctaatgcaatattctagaatttctgaacttc----taaaattagtgttatattttcccttaaatttgaca-ttgttaggatgatataattattttctgcagATCTTTCCACCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG----------------------------------

upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 26
-gtaacaagcaacttctt---atcttttacattatagtcaatcttttcatggtcctaagatgatggcttcttgataccgtatctcctgatgaaattcttgcaaccctttgaagtataatgacca--attaatccaatgtgctggtatgccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACTTTACGAGCTGAGGAGGTATATTACTAGGCTGCACCTTGTATTTTTCTTA
  |  |     | || |    |   |||||   ||    | || |  | |  | ||||    |||   |     | | | || |     | |||||  ||  |   |||    || | |   ||   ||| |   || |  |  |||    |||||||||| ||  |   ||| |  || ||||| |||||||| ||||||||||| |||||||||||||||                                  
gtttgcgcatgatttatgtgaagtatttaccgaatgaagagtcctggc-tctttctaatccaatgttctagaatttctgaattt----gtaaaattagtgttatttttttccttaaacttggcattgttagtatgatataat--tattttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG----------------------------------

upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 26
gtaacaagcaacttcttatcttttacattatagtcaatcttttcatggtcctaagatgatggcttcttgataccgtatctcctgatgaaattcttgcaaccctttgaagtataat-gaccaattaatccaatgtgctggtat---gccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACTTTACGAGCTGAGGAGGTATATTACTAGGCTGCACCTTGTATTTTTCTTA
                                          ||||| ||     || ||   |   | | |   ||||   |       ||||| |||||  ||    | || | |   |  ||   || | |||||  ||   ||||||||||| || ||| | | ||||| ||| ||||||||||||||||| ||||||||  | || || ||||||| |                               
------------------------------------------tcatgttc----aataat--ttgaataaaattttatccattc------ttctttcaacctcttcttttctacttggttatatagctcattatgctgtgatattgccttgcagATCTTTCCACCCAGTGAAAAAATCGAGAATATAAATGACCAATACTGGACACTCCGTGCAGAGGAGGCAA------------------------------

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|125250765|gb|EL264850.1|EL264850
EST:     TGTTTTACCACAAGATCTACAAG                         ATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACT
genomic: TGTTTTACCACAAGATCTACAAGgtaacaagca ... tgccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACT
EST: gi|164219023|gb|ES110085.1|ES110085
EST:     GGTGTTTTACCACAAGATCTACAAG                         ATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACT
genomic: GGTGTTTTACCACAAGATCTACAAGgtaacaagca ... tgccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACT
EST: gi|163972684|gb|ES085266.1|ES085266
EST:     TTGCTCGAGGTGTTTTACCACAAGATCTACAAG                         ATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACT
genomic: TTGCTCGAGGTGTTTTACCACAAGATCTACAAGgtaacaagca ... tgccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaccctttgaagtataatgaccaattaatccaatgtgctggtatgccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACTTTACGAGCTGAGGAGGTATATTACTAGGCTGCACCTTGTATTTTTCTTA
                        aattaat  putative branch site (score: 3)
           aagtataat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaagcaacttcttatcttttacattatagtcaatcttttcatggtcctaagatgatggcttcttgataccgtatctcctgatgaaattcttgcaaccctttgaagtataatgaccaattaatccaatgtgctggtatgccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACTTTACGAGCTGAGGAGGTATATTACTAGGCTGCACCTTGTATTTTTCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG