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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagctcaattcgatttcgcttgtgttgtgatgttctgtgtcttcatttagcagtacttatgtgtgttctgtcgtgtttcttgattcagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAGTCTTAGATGTTGGGTGTGGCATTGGTGGAGGTGACTTCTACATGGCTGA

Basic information

species Arabidopsis thaliana
transcript AT3G18000.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g47545.1 (Oryza sativa), 3'ss of exon 7
gtaaaagctcaattcgatttcgcttgtgttgtgatgttctgtgtcttcatttagcagt--acttatgtgtgttctgtcgtgtttcttgat--tcagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAGTCTTAGATGTTGGGTGTGGCATTGGTGGAGGTGACTTCTACATGGCTGA
                     |   ||      || | || || ||  ||| |   ||  || | |     |||   | || || |||||   |||| || || || ||||||||||| ||  || |||| ||||| |||||||||||  | ||||||||||| || ||||| || || |||||||| ||||||||
---------------------gtcagttgaacaatttcct-tgcctctattaaaatgtcaacatttactcattcaaacatgcttattgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA

upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G122296_T01 (Zea mays), 3'ss of exon 7
gtaaaagctca-attcgatttcgc--ttgtgttgtgatgttctgtgtcttcatttagcagtacttatgtgtgttctgtcgtgtttct-tgattcagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAGTCTTAGATGTTGGGTGTGGCATTGGTGGAGGTGACTTCTACATGGCTGA
|| | ||  || || |  ||| |   || | ||||||| |  | |||         ||||| |   |   |||| |      |  || ||   ||||||| || |||||||||||||||||| ||||||| || || || ||||| ||  | |||||||| ||||| ||||| ||||||||||| || ||||||||
gtgagaggacacatccctttttgtcatttttttgtgatatcgtatgt---------gcagtgccattaaatgttattattcatcactatgcaccagAGACTACAAAAGAATTTGTGGAGAAACTGAATCTTAAGCCTGGGCAGAAGGTGCTTGATGTTGGATGTGGAATTGGGGGAGGTGACTTTTATATGGCTGA

upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G060886_T01 (Zea mays), 3'ss of exon 7
gtaaaagctcaattcgatttcgcttgtg--ttgtgatgttctgtgtcttcatttagcagtacttatgtgt-gttctgtcgtgtttcttgattcagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAGTCTTAGATGTTGGGTGTGGCATTGGTGGAGGTGACTTCTACATGGCTGA
|| |  ||   | ||  | |   || |   |||||||||||| |   | ||||  |   | ||||  ||| ||| |||     |     |  ||||||| || |||||||||||||| ||  || |||| ||||| ||||| || ||  | |||||||| ||||| ||||| ||||||||||| || ||||| ||
gtgagtgcggcaatccctgttaattttaacttgtgatgttctat--ttgcattgtg---tccttaaatgttgttatgtatcactgtccaa--cagAGACTACAAAAGAATTTGTGGACAAGCTGGATCTCAAACCTGGACATAAGGTGCTTGATGTTGGATGTGGAATTGGGGGAGGTGACTTTTATATGGCCGA

upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0011g05220.t01 (Vitis vinifera), 3'ss of exon 6
----gtaaaagct-caattc----gatttcgcttgtgttgtgatgttctgtgtcttc-atttagcagtacttatgtgtgttctgtcgtgtttcttgattcagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAGTCTTAGATGTTGGGTGTGGCATTGGTGGAGGTGACTTCTACATGGCTGA
    | | ||  | | ||||    ||  |   | || |  | |  |    |   ||| | ||| || | |||            ||  |  | ||||| |||| ||||| || ||||||||||  ||  || | || || || || ||||||||| | || || || ||||||||||| |||||||||||||||||||||||
ctaagcacaaattgccattcatgagaaattattcgtttaattaactataataaattccaattaccaattcttgcactgagaaaatcccgaat-ttgat-cagAAACAACAAAGGAATTTGTGGCTAAGTTGGAGCTTAAGCCCGGCCAGAAAGTCCTGGACGTAGGTTGTGGCATTGGCGGAGGTGACTTCTACATGGCTGA

upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0011g05200.t01 (Vitis vinifera), 3'ss of exon 7
---gtaaaagctcaattcgattt-cgcttgtgttgt-gatgttctgtgtcttcatttagcagtacttatgtgtgttctgtcgtgtttcttgatt----cagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAGTCTTAGATGTTGGGTGTGGCATTGGTGGAGGTGACTTCTACATGGCTGA
   ||   ||   ||    |||| |||     |||  | |  |     |  | |  |   | || || |   | |    |    ||  ||||||    |||| ||||| ||||||||||||   ||| || | || || ||  | || || ||| ||||||| || |||||||| ||||||||||||||||||||||| ||
ccagtttcagtcaaacaaaattttcgcaatcattggaggttattcacattcttaactgcaactaatt-taaatttctctttaccttatttgatttgaacagAAACAACAAAAGAATTTGTGACAAAATTGGACCTTAAGCCTAGCCAAAAGGTCCTAGATGTAGGCTGTGGCATCGGTGGAGGTGACTTCTACATGGCAGA

upper sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv17s0000g02430.t01 (Vitis vinifera), 3'ss of exon 7
--gtaaaagctcaattcgatttcgcttgtgttgtgatgttctgtgtcttcatttagcagtacttatgtgtgttctgtc-gtgtttcttgatt------cagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAGTCTTAGATGTTGGGTGTGGCATTGGTGGAGGTGACTTCTACATGGCTGA
  |  ||   | |  | | ||||     |  | |||  ||| ||| |||  || |  |||| |  | |   |||| |  |||   | || |       |||||||||| |||||||||||||  ||| || | || ||||| || ||||| ||| ||||||| || ||||||||||| |||||||||||||| ||||| ||
cagataattattagctggttttcatgaatcatttgaaattcagtgactt-gttaattagtattcttctaatttctttgagtgaaccctggtctttgagcagAGACAACAAAAGAATTTGTGGGAAAACTGGACCTTAAACCTGGCCAGAAGGTCCTAGATGTGGGCTGTGGCATTGGAGGAGGTGACTTCTATATGGCAGA

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|47829217|gb|CK118901.1|CK118901
EST:     ACGCTATGAGCGTGTCTTTGGCCAAGGGTTTGTGAGCACTGGTGGACTTG                         AGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAG
genomic: ACGCTATGAGCGTGTCTTTGGCCAAGGGTTTGTGAGCACTGGTGGACTTGgtaaaagctc ... cttgattcagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtgtcttcatttagcagtacttatgtgtgttctgtcgtgtttcttgattcagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAGTCTTAGATGTTGGGTGTGGCATTGGTGGAGGTGACTTCTACATGGCTGA
                                            tcttgat  putative branch site (score: 4)
                                        tgtttctt  CT-rich tract
        ttcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagctcaattcgatttcgcttgtgttgtgatgttctgtgtcttcatttagcagtacttatgtgtgttctgtcgtgtttcttgattcagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAGTCTTAGATGTTGGGTGTGGCATTGGTGGAGGTGACTTCTACATGGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG