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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacaatgatttgaattcacaagtaacctttttatgttgctatgttgtttgcctttttcgtgtcctttgtaatggaagaacctttgatttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG

Basic information

species Arabidopsis thaliana
transcript AT1G43130.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 3
acacaatgatttgaattcacaagtaacctttttatgttgctatgttgtttgcctttttcgtgtcctttgtaatggaagaacctt------tgatttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG
        | ||  || ||||| ||   | || |||   |  ||    |  | |    |   |       |||| |   ||||       | || ||  ||  |||| |||||||| || || |||||||| || || || || ||||| || |||||||||||||| |||||||||||||| |||||| | ||    ||||||
----gtatacttccatacacaaata---tattcatgacacattgacactatcatcagccacattggaca-aatgaacttacctcataaaatcatcttgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG

upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g36110.2 (Oryza sativa), 3'ss of exon 4
--acacaatgatttgaattcacaagtaacct-ttttatgttgctatgttgtttgcctttttcgtgtcctttgtaatggaagaacctttgatttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG
  | |   | || |    |   ||  |   | ||  | ||| | |  ||  |||  |  ||| | | ||     | | |       ||  || || ||  |||| ||||| || || || |||||||| || ||||| ||  |||| || |||||||||||||| ||||||||||| || |||||  || |||  ||||||
tgataggttaatgtatcattttaatcattatattacaagtttccaactttgttg--taattcattttctcaacca-gaattttttcttatttcttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTATTGGTGAATATGCATTTGGATTCATAACATCGACGATGATCCTTCAG

upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 4
--acacaatgatttgaattcacaagtaacctttt-tatgttgctatgttgtttgcctttttcgtgtcctttgtaatggaagaacctttgatttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG--
  | |   | || |    |   ||  |   | ||  | ||| | |  ||  |||  |  ||| | | ||     | | |       ||  || || ||  |||| ||||| || || || |||||||| || ||||| ||  |||| || |||||||||||||| ||||||||||| || |||||  || |||  ||||||  
tgataggttaatgtatcattttaatcattatattacaagtttccaactttgttg--taattcattttctcaacca-gaattttttcttatttcttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTATTGGTGAATATGCATTTGGATTCATAACATCGACGATGATCCTTCAGGT

upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G149662_T01 (Zea mays), 3'ss of exon 4
acacaatgatttgaattcacaagtaacctttttatgttgctatgttgtttgcctttttcgtgtcctttgtaatggaagaacctttg----att--tttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG
      | |      |||    | |  | |||  | ||  |||   ||||    |||   | |  |||| |   ||| |    ||     |||  | |||| ||||| ||||| || ||||| || ||||| || ||||| || ||||| || || ||||||||||| ||||||||||| || |||||| | |||   ||||||
-----gtcaggcagcttcttttgcatgcatttcttttt-ttataa-gtttaa--tttaaatatattttgcagaagaatatttcttatgtaattattctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACTGTGGTCCTTCAG

upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 4
acacaatgatttgaattcacaagtaacctttttatgttgctatgttgtt-tgcctttttcgtgtcctttgtaatggaagaacctttgatttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG
        ||    ||   ||  |    ||| | |    || | ||||  | ||||||    | |     |  |   || || |||  ||| | |   |||| ||||| || || || || ||||| |||||||||||  |||| || ||| |||||||||| ||||||||||| || |||||| |  ||   ||||||
-tgtttacatagatatcagcagtttgtatttgtttccaactttcttgtagttccttttgtcaggcagaaatgttcttaggactttttttttctctggacagATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG

upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 4
acacaatgatttgaattcacaagtaacctttttatgttgctatgttgtttgcctttttcgtgtcctttgtaatggaagaacctttg----at--ttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG
               |    ||| | || ||  |||| | |   || |||   ||||     |  |||| |   ||||     ||     ||  ||||||| | ||| ||||| || || || || ||||| || ||||| || ||||| || || ||||||||||| ||||||||||| || |||||| |||||   ||||||
--------------gtcaggaagcatccattgcatgt-gtttctttttttatattttaaagatagtttgcacaagaagttttcttatgtaattattttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG

upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
acacaatgatttgaattcacaagta-acctttttatgttgctatgtt-gtttgcctttttcgtgtcctttgtaatggaagaacctttgatttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG
  |  || |||    | ||   ||  |  | | |   || | ||||| |   |  ||| |  |   | |   | |   |   |  ||   | || ||  |||||||||| || ||||| |||||||||||||| ||||||||||| || ||| |||||||||| |||||||| |||||||||||| | || |  ||||||
--agcataattgtgctccatgtgtttatatatgtggtttacaatgttagcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG

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|164027665|gb|ES065363.1|ES065363
EST:     CTATTTCTCCAG                         ACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTA
genomic: CTATTTCTCCAGgtaagactgt ... ttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTA
EST: gi|116425168|gb|EG467760.1|EG467760
EST:     CAAGCACATATATTCAGCTTCTAAGCAAATTAGCAATGCTATTTCTCCAG                         ACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTA
genomic: CAAGCACATATATTCAGCTTCTAAGCAAATTAGCACTGCTATTTCTCCAGgtaagactgt ... ttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTA
EST: gi|116425169|gb|EG467761.1|EG467761
EST:     CAAGCACATATATTCAGCTTCTAAGCAAATTAGCACTGCTATTTCTCCAG                         ACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTA
genomic: CAAGCACATATATTCAGCTTCTAAGCAAATTAGCACTGCTATTTCTCCAGgtaagactgt ... ttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTA
EST: gi|164096707|gb|ES135328.1|ES135328
EST:     CTATTTCTCCAG                         ACCAAAACACTACTGCCTTTAAAGTAGGTAGCAATCATCCGTCACCCTCGT
genomic: CTATTTCTCCAGgtaagactgt ... ttgttctcagACCAAAACACTACTGCCTTTAAAG-AGGTAGCAATCATCCGTCACCCTCGT
EST: gi|116447062|gb|EG489654.1|EG489654
EST:     CAAGCACATATATTCAGCTTCTAAGCAAATTAGCACTGCTATTTCTCCAG                         ACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTA
genomic: CAAGCACATATATTCAGCTTCTAAGCAAATTAGCACTGCTATTTCTCCAGgtaagactgt ... ttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgcctttttcgtgtcctttgtaatggaagaacctttgatttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG
                                    ctttgat  putative branch site (score: 5)
                                          tttttgttctc  CT-rich tract
                                     tttgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacaatgatttgaattcacaagtaacctttttatgttgctatgttgtttgcctttttcgtgtcctttgtaatggaagaacctttgatttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG

acacaat
- - - -gatttga
- - - - - - - attcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaac