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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtagatgaagattgtgagagcaagaacttagtttcccaaaaaaaagttgcttgcttcgcatttgcccgatatgcatagtctcacaatgccttattgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA

Basic information

species Arabidopsis thaliana
transcript AT5G67560.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
agtagatgaagattgtgagagcaagaacttagtttcccaaaaaaaagttgcttgcttcgcat-ttgcccgatatgcata-gtctcacaatgccttat-tgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA
  |    |   | |    |   |     ||||      |||   |  |   ||| | |  || ||||  |||  | ||    |  | | | | |||| ||||| || || ||||||||||| ||||||||||| |||||||| ||||||||||| || || ||||| ||||| || ||  |||| 
catgtgggccaacttctggtttata---ttagcgagtaaaatggatatgctttgttactaatattgcttgatgaggattcaacatatattcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT

upper sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G007188_T01 (Zea mays), 3'ss of exon 1
-------agtagatgaagattgtgagagcaagaacttagtttcccaaaaaaaagttgcttgcttcgcatttgcccgatatgcatagtctcacaatgccttattgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA
        ||| ||| |     |||  | ||     |  |       |   ||| ||||||| | || ||       |||   |  | |    |   ||    |||||||||||||||||||||| ||||||||||||||| |||| || |||||||| || || ||||||||||| |||    |||| 
taacacttgtaaatggatgaactgat-gtaatcttctgctcctttcgattcaaggtgcttgcct-gc-ttgaataactatttctgctttttttacatct----gcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT

upper sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
-------agtagatgaagattgtgagagcaagaacttagtttcccaaaaaaaagttgcttgcttcgcatttgcccgatatgcatagtctcacaatgccttat-tgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA
        ||| ||| |     ||| |  |   ||      |  | |   ||||   ||||       | |||  || ||   |  |   ||  |     || ||||||||||||||||||||||| ||||||||||| |||||||| || |||||||| || || || |||||||| |||  | |||| 
gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaaggaccttg-------tctgcttga-ataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT

upper sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 1
agtagatgaagattgtgagagcaagaacttagtttcccaaaaaaaagttgcttgcttcgcatttgcccga--tatgcatagtctcacaatgccttattgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA
  |   ||||  |  |      || ||  |  ||    ||| | |  |    ||   | || ||| |     | | | |  |     | |    |  ||||||||||| ||||| |||||||||||||| || |||||||| ||||| ||||||||||| ||||||||||| || ||| |||||
cttgcctgaaattacttctgataaaaaaat--ttatttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA

upper sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ23242 (Selaginella moellendorffii), 3'ss of exon 1
agtagatgaagattgtgagagcaagaacttagtttcccaaaaaaaagttgcttgcttcgcatttgcccgatatgcatagtctcacaatgccttat-tgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA
                                          |      |     | |    |||      |   ||  |||   | ||  |  | || |||||||||||||||||||| |||||| | ||| | |||||||| ||||| || || ||||| || ||||| |||    | || 
----------------------------------------gtatggagcgtcgaatccatgcttgggtctcaca-attctcttggattgattgctctgtagCCTCTTCTTCAAGCAAGAGATGGAGTTATCAGTAATAGGACTACAAAAGGCTGGCAAGACGTCCCTTGTCAACTCCATCGCT

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|124877019|gb|EH956456.1|EH956456
EST:     TGCTCTTCTCAATTGGCTTCGCAG                         CCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGC
genomic: TGCTCTTCTCAATTGGCTTCGCAGgtcagtttct ... cttattgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGC
EST: gi|125274083|gb|EL288168.1|EL288168
EST:     CAATTGGCTTCGCAG                         CCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGC
genomic: CAATTGGCTTCGCAGgtcagtttct ... cttattgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgcttgcttcgcatttgcccgatatgcatagtctcacaatgccttattgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA
                                 gtctcac  putative branch site (score: 3)
                                            ccttatt  putative PPT
                                              ttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtagatgaagattgtgagagcaagaacttagtttcccaaaaaaaagttgcttgcttcgcatttgcccgatatgcatagtctcacaatgccttattgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA

- - -atgaaga
- - - - - - - - - - -caagaac
- - - - - - - - - - - - - - - - - - -caaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcacaa