Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatatacactctcatcctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgacttttctcttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG

Basic information

species Arabidopsis thaliana
transcript AT2G01250.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 5
gtatgtatatacactctcatcctaaaccctttaatct-----gatgctatgagataacaagagtcttg---aagagtgtgacttttctcttctgtttt--tcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG
    |  |   ||   | |   || | | ||| | ||     ||| ||  |  ||    |  ||  |        |  | |  |  ||  |||| | |  |||| | ||| ||| |||||||||||| |||||||||||||||||| |||||||||||||| ||| | ||||||||  || |     |||||    |  | |||
----gggttctcatagtgactttatagcttttgagcttgttagatacttggttatttttaatgttctacctggctgaatcaagtaccttctctggtgtgatcagGTACCCAAACCTGAAGAGTGTCAGGGAATTGATCTACAAGAGGGGTTACGGAAAGCTCAACAAGCAGAGGATTCCTCTTCAGAACAACAAAGTCATTGAG

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G094051_T03 (Zea mays), 3'ss of exon 5
-----gtatgta-tatacactctcatcctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgacttttct--cttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG
       ||  |  | ||| |  |      |   | |  |||| | |||  | ||   ||   |  |   |     | |||    |  |   | || || || | ||| |||||||||||||||| ||| |||||||||||||| || || |||||||| ||| | ||||||||  || || |  |||||    |  | |||
aaaaaacataaagcagacagtgcctggagtagttcctgcatctta-gcttggtgact-catctgcttctgatgaccttactaaagtggcaaatcttgtttagGTACCCAAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAAGCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
-gtatgtatatacactctca---tcctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgacttttctcttctgtttt--tcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG
   |  |   |||| |   |   ||   |     ||| |       |    | | ||   ||  |   |     |  ||   ||  | | | ||  | || | ||| |||||||||||||||| ||| |||||||||||||| || |||||||| || ||| | ||||||||  || || || |||||    |  | |||
aaaacattgctacaataggagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G178807_T03 (Zea mays), 3'ss of exon 4
---gtatgtatatacactctcat----cctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgacttttctcttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG
     |  |   |    ||| ||       |||||    | ||   |  | |   || |  |  |||  ||||  ||    | | |  |||   | | ||||| ||| ||| |||||||||| | ||||||||||||||| |||||||| || ||||| ||| | ||||||||  |  | |   |||||  | |  | |||
gcaccaaatccctgagttctgataattttcaaaccagaaattccacttgtttatcattatgat-gtccagaagcatgaacatctacctttcatctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGGGAAGCTGAACAAGCAGAGGATTCCGCTTAGCAACAACAATGTCATCGAG

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G100225_T01 (Zea mays), 3'ss of exon 4
--------gtatgtatatacactctcatcctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgacttttctcttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG
         | | | | |  |     || |  ||      |||  |   | || |          ||| |||||  ||  | | |    |||   | | ||||| ||| ||| ||||||| || | ||| || |||||||||||||||||||| ||||| ||| | ||||||||  |  | |   |||||  | |  |||||
ccagatccctgttttttttaaaaaaaattcgcaagtaagaaattcgggtcgattatcgttgtgatgtcctgaagtctggaaatgtatgtttcg--tctccagATACCCCAACCTGAAGAGCGTTAGGGAGTTAATCTACAAGAGAGGTTACGGGAAGCTGAACAAGCAGAGGATTCCACTTAGCAACAACAGTGTCATAGAG

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
-------gtatgtatatacactctcatcctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgact--tttctcttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG
       | ||  |   | ||| ||      |   | |  |||| | |||  | ||   ||   |  |   |     | |||    |  |   | || || || | ||| |||||||| ||||||| ||| |||||||||||||| || || ||||| || ||| | ||||||||  || || |  |||||    |  | |||
gaaaaaagcataaa-gcatactgtctggagtagttcctgcatctta-gcttggtgact-catctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 5
gtatgtatatacactctcatcctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgacttttctcttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG
||| ||  |    |    |   | |  |   |  |    | |        | || |  |||| |    ||  | |   ||          |||| | |||||| ||||||||||| |  ||||||||||||||||| || || |||||  ||||| | ||||| || |||||||| |||||||||||| | || 
gtaagtgaaagttcaactacattgattctcatggttcattacct----gcaccatggttcttaatatttgcaaatccact----------tcagGTACCCTAATTTGAAGAGTGTTAGAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCTTTGACAGACAACTCTATTATTGAA

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 5
gtatgtatatacactctcatcctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgacttttctcttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG
    |||  |  |   ||| |      | || | | | ||   |||    |  |   |       |  | | | | ||  |   |    ||||| | |||||| ||||||||||| || ||||||||||||||||| || || |||||  ||||| | ||||| || || || | ||||||||||||||| || 
----gtaagtgaaagttcaac----gacattgattgtcat---atggttcattacctgcaccacgggttcttaatatttgcaaatccacttcagGTACCCTAATTTGAAGAGTGTAAAAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAA

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|125291465|gb|EL305550.1|EL305550
EST:     TGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
genomic: TGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
EST: gi|164018459|gb|ES143570.1|ES143570
EST:     CCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGTAGTTGTCAAGGAATTGATCTACAAGAGAGGTTAC
genomic: CCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAG-AG-TGTCAAGGAATTGATCTACAAGAGAGGTTAC
EST: gi|125219533|gb|EL233618.1|EL233618
EST:     AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTANAAGAGA
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGA
EST: gi|86083519|gb|DR379278.1|DR379278
EST:     TTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
genomic: TTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
EST: gi|164108779|gb|ES025314.1|ES025314
EST:     AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAG
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAG
EST: gi|124980897|gb|EL053809.1|EL053809
EST:     CCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
genomic: CCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
EST: gi|164154234|gb|ES205087.1|ES205087
EST:     AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAGCTTGAAGAGTGTC
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTC
EST: gi|125307633|gb|EL321718.1|EL321718
EST:     CGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGGTCTACAAGAGAGGTTACGG
genomic: CGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
EST: gi|164231700|gb|EL998579.1|EL998579
EST:     AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAG
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAG
EST: gi|164207272|gb|ES175042.1|ES175042
EST:     CCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
genomic: CCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
EST: gi|124719583|gb|EH810985.1|EH810985
EST:     TGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
genomic: TGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
EST: gi|124745629|gb|EH836441.1|EH836441
EST:     AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACT
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACT
EST: gi|125205577|gb|EL220531.1|EL220531
EST:     GAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGG
genomic: GAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGG
EST: gi|86082419|gb|DR378178.1|DR378178
EST:     AAGGCTACGATGAACAT-STTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
EST: gi|164094463|gb|ES082960.1|ES082960
EST:     ACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAG
genomic: ACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAG
EST: gi|164237567|gb|ES093249.1|ES093249
EST:     AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTC
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTC
EST: gi|124934660|gb|EL011713.1|EL011713
EST:     AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTG
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTG
EST: gi|125226913|gb|EL240998.1|EL240998
EST:     TGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
genomic: TGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
EST: gi|86082295|gb|DR378054.1|DR378054
EST:     AAGGCTACGATGAACAT-STTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
EST: gi|47828829|gb|CK118513.1|CK118513
EST:     AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGG
EST: gi|125094418|gb|EL151918.1|EL151918
EST:     AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG                         ATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAG
genomic: AAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGGgtatgtatat ... tgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctatgagataacaagagtcttgaagagtgtgacttttctcttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG
       agataac  putative branch site (score: 3)
                               tgacttttctcttctg  putative PPT
         ataacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatatacactctcatcctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgacttttctcttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT