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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG

Basic information

species Arabidopsis thaliana
transcript AT1G30470.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 15
-actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG-----------------------------
 |    |  |  |   | || |  |  | |  |    ||  |  ||    | |  ||   ||   | ||          |   ||    |     || ||||||||||| |||||||||||||| ||||| ||||| ||||| ||  |||| || |||||||| |||||  |                             
aaagaacagaatgttgcatgcggataatatagtgtctaga-accatatttgttgaagctgtacttttgagtgagtggatttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGGTAATTTGTGATCTTAAAACATACTTTGG

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os01g40340.1 (Oryza sativa), 3'ss of exon 15
-actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG
 |    |  |  |   | || |  |  | |  |    ||  |  ||    | |  ||   ||   | ||          |   ||    |     || ||||||||||| |||||||||||||| ||||| ||||| ||||| ||  |||| || |||||||| |||||  |
aaagaacagaatgttgcatgcggataatatagtgtctaga-accatatttgttgaagctgtacttttgagtgagtggatttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 17
---------actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG
         ||| |   | |   |    ||  |||  | ||   |||| | |||  | |  ||   ||||   |  || |     |  ||      || |   || |||||||||||||||||||||||||| || ||||| || ||||| || |||||  | || ||||| ||||| ||
gaatctagtactagtataacaagtgtgttg--tgtcctgatgtccagcaagtataaatgtattttcgatagtctgaatttctgtgctcct------gtttccttt-cagGATGTCTACTTTGATGATGAATCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAG

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os01g40370.1 (Oryza sativa), 3'ss of exon 4
---actcgctcagcggctcctgtgcctgtttttataagcagccaa---tatggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG----
   |    |  |  |   | || |     |  | |    | |||    | | |||||| || |  | ||  |||  || |   |  || |    ||    || ||||||||||| |||||||||||||| ||||| ||||| ||||  ||  |||| || ||||||||||| ||  |    
aaaaagaacggaatgttgcatgcggaaaatagtgtctataaccatatttgttgaagctgtact--tctgacaga-gtggatttccattgttttctcc---tttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCAAGATGGGTAA

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os01g40390.1 (Oryza sativa), 3'ss of exon 6
-actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG-----------------------------
 |   |    |    |    |||   |  |  |    ||  |  ||    | |  | |  ||      |          |   ||    |     ||  |||||||||| |||||||||||||| ||||| ||||| ||||  ||  |||| || ||||||||||   | |                              
aaaaagaatggaatgttgcatgcggataatagtgtctaga-accatatttgttgaaattgtacttctcactgagtggatttccattgttttctccttttagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCTTAAAACTTACTTTGGTATCCTCTTTTTTTTTTTGC

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G096107_T01 (Zea mays), 3'ss of exon 18
actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagat-atgaaaacctcttatgaa-gtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG
      ||||    | ||||   | ||  |   | ||      || |||   | |      ||||   | |||     ||||  | |   | | ||  ||||||||| || |||||||||||||||||||| || || || |||||| | ||||||||||| ||||| || ||
gtatattcag-atttactgtttatattcattgtatcatttcgaattgaa--ctgaacagattggtgtttgatgtttttctctggttattatatctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGCCTTGGAGACGACCAAGAAAG

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G000039_T01 (Zea mays), 3'ss of exon 18
actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaa--gctttagtgatatggt---agatatgaaaacctcttatgaagtctatgtt----gcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG
      ||||  | | ||||     ||  |   | || |    || |||  |      |  |||      |  | |||     | || ||     ||| |      |||||||| || |||||||||||||||||||| || || || |||||| | ||||||||||| ||||| || ||
gtatattcagaag-tactgtttagattcattgtatcatcttgcattgaactgaacagattgtatctcctgatgtttgatgtttttttctggttattatatctgccacagGATGTATATTTTGATGATGAATCTGCAGAGGTTGTAATCTCCTCCCTTCGCCTTGGAGACGACCAAGAAAG

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G149321_T01 (Zea mays), 3'ss of exon 8
--actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG
  |   |    ||      | ||     | || |       |||   | ||    | |   |    ||    || |    | || |  | ||| | |  |||||||| || |||||||||||||| || || || || ||||| || ||||| || |||||||||||||| ||
ggatatgaagtgcaataaatatgaactatattgtttttgctcaagtagaaaaaggttgaacttctatatcagtggactgtttttcttcattctcttt--cagGATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAG

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
-actcgctcagc--ggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagatatgaaa-acctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG
  || | |  |     | | | ||  ||| | | |  |       | | || | || | |  || | |    || ||| | ||   || |  | ||| |||||||||||||| ||||||||||||||||||||||| || ||||| || |||||  | ||||||||||| || ||
ttctagttttgtttaacacttatga-tgtatct-tgggatttttttgttgaggtttgatt--tacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagct---ttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG
  | | | ||  |   |||  |   | || ||||||      | ||  | |      |||  | ||  | ||   | | | ||||||| ||  | | | ||||||||||||||||||||||||||| || ||||| |||||||| ||  ||||  | |||||||| ||||||||
cattgtttagtcg--actgctctcatgttcataagccattgctttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagattct-tggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG

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|164065874|gb|ES116146.1|ES116146
EST:     GCCCAAGGCTCTATGGAACGCGATGATGAG                         GATGTCTACTTTGATGATGAATCTGCAG
genomic: GCCCAAGGCTCTATGGAACGCGATGATGAGgtattgttcg ... tatgttgcagGATGTCTACTTTGATGATGAATCTGCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG
                      atatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA