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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttccaatgttttggaatgtttagaactgatgactatttatgtccaaatcacggatataacttataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG

Basic information

species Arabidopsis thaliana
transcript AT3G53520.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 3
-gtttccaatgttttggaatgtttagaactgatgactatttatgtccaaatcacggatataact--tataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
    | ||||  | | |   || | | |    |   |   |    |    |      |||| ||  | || ||    |  |||||||  || | |   | |||||  | |||||||| |||||||| |||||||| ||  ||||||| || |||||||| ||||| ||||| || ||||||||||||
ttgctgcaatactgtagttcgtattgtagcattatgtgacttcaacatcttagtaactatagctattctacgatcttttgctaactgacttatta---tgcagGTGCGCATTGCTCGCATTTTCAATACATATGGCCCTCGAATGTGTCTAGATGATGGCCGTGTGGTTAGCAATTTTGTTGCCCAG

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 3
gtttccaatgttttggaatgttta-gaactgatgactatttatgtccaaatcacggatataacttat--aagagtgatctctaactgcat-tttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
 ||| | |  | ||    |||||| |   |||  |  ||   || | |    | || |   | ||||  |||||  | ||  |    ||  | |   |  |||||| |||||||| || || |||||||||||||| ||  | |||||  | ||||||||||| |||||||| ||||| || || |||
-tttaccacatgttt---tgtttatgtgttgagtaacatcattgcctactgaatggtttccatttattaaagagaaaacttgactaacaaatgtttctcctcagGTGAGAATTGCGCGAATATTCAACACATATGGCCCTCGTATGTGTTTAGATGATGGGCGAGTTGTTAGCAACTTCGTCGCTCAG

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 3
--gtttccaatgttttggaatgtttagaactgatga-ctatttatgt-ccaaatcacggatataacttataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
   ||    || | ||| |||| |     || | ||  | | | ||| |   |||     | |    |  |||||  | || | ||    | | |     |||||| |||||||| || || || ||||||||||| ||  |||||||  | |||||||| || |||||||| ||||||||||| |||
tctttgtttatatgttgcaatgat----gcttacgagttgtctgtgtgctttatctttattctcttcttgaagagcaaactttgacatactgtgcttccctcagGTGAGAATTGCACGCATATTTAACACATATGGCCCTCGAATGTGTTTAGATGATGGCCGAGTTGTTAGCAACTTTGTTGCACAG

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G05260.1 (Glycine max), 3'ss of exon 3
gtttccaatgttttg----gaatgtttagaactgatgactatttatgtccaaatcacggatataacttataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
    | |||  ||        ||   | ||| | |  |||| |||||   ||||   | | || || | | |  | || |  |   ||  ||     |||  ||||| | |||||||| ||||||||||||||||| ||| | |||||  | |||||||||||||||||||| || |||||||| |||
aaaacaaatagttaatcatagataagtggaattta-aactacttatgga-aaattctgcaaattacatgttattgagaccgat--ttggtttgatggtttatagGTTCGTATTGCTCGAATTTTCAACACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTTGTTAGCAATTTTGTTGCACAG

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 3
---gtttccaatgttttgga-atgtttagaactgatgactatttatgtccaaatcacggatataacttataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
    ||   | |   |   | ||   |  || | |  ||||  ||||   ||||   | | || |   ||   | |||     | |||   |     |||  ||||| | |||||||| |||||||| |||||||| ||| | |||||  | |||||||||||||| ||||| || |||||||| |||
aaaattagtagttaatcacacataagtgaaattta-aactacctatggt-aaattttgcaaattaa--atgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 4
-gtttccaatgttttggaatgtttagaactgatgactatttatgtccaaatcacgga-tataacttataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
  |   | ||   ||  ||  | ||    |  ||  ||  ||| |||| |    ||| | ||    |||     |||   | |||| ||||||  ||  |||||  | || || || |||||||| |||||||||||  | |||||  |||||||||||||||| ||||| || |||||||| |||
aatgggccat-ccttataacttctact-ttactgtatagatatctccataaagtggactgtagacaatagtttggattaatcactgaattttctgttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S120_28V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------gtttcca----atgttttggaatgttta---gaactgatgactatttatgtccaaatcacgga------tataacttataagagtgatctctaactgca---ttttcaattttc----------agGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
                                     | |||||     | ||  | | | ||||   ||| |  | |  || | ||        |  ||        ||  | ||   | |   || ||   | |    |    || |||          ||||| | || || || ||||||||||| ||||| || ||||||||| ||||||||||  | ||||| |||||||||||||| |||
gtgaagtgacttggcttcagtaattgtgtagagtttggcttccatttagtcttacgcattttttattggaagttgtaataatatgtgatgggtcaattgagtttttcgtacttgattgcattatactttagtcgtaatgctcctgatgttcggaggcatgcagGTTCGGATCGCCCGCATTTTCAACACTTATGGACCAAGAATGTGCATTGATGATGGTAGGGTTGTCAGTAACTTTGTTGCTCAG

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S120_29V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------gtttccaatgttttggaatgtttagaactgatgactatttatgtccaaatcacggatataacttataagagtgatctc------taactgcatttt-caatt--ttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
                                                             ||||    | ||||    | ||||    ||  || |    |     | || | | |   |   |||   | || | |       |  ||| | ||| ||||   | |||||| | |||||||||||||| ||||| ||||| || || |||||| | ||||||||  | |||||||||||||| ||||| |||
gtgatttattttattttattttatttttttgttttaatttgttttgttttgttttgtttttgtttttggtttttt---ttttttaattttggagaatgccgagtctaagattaggaaagca--ctatggcattggttttagcgtatggctgaaatttgcaatgggtgcagGTTCGCATTGCTCGTATTTTTAACACTTATGGACCAAGGATGTGCATCGATGATGGCAGGGTTGTTAGTAACTTCGTTGCTCAG

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------gtttccaatgttttggaatgtttagaa----ctgatgactatttatgtcca--aatcacggatataacttataagagtgatctctaactgcattttcaatt--ttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
                                                             |||   | ||  | ||| | |  | |    ||| ||    | ||  || |  ||||||  |  |    | |    |  |  | |   ||   ||| || |  | |||||| | ||||||||||||||||| || ||||| || ||||||||  ||||||||||  | ||||| || ||||| || || |||
gtacagtccgaattttcatggattttgaatatgcagtggcagtagtttacggtaagttccatttaggaagtcatcgaaggctatggattagctggtggagttctaattcgagaaatcacaaaggtgttgttttgctgcaaggttt--ttgaggtttgaagtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ23020 (Selaginella moellendorffii), 3'ss of exon 3
gtttccaatgttttggaatgtttagaactgatgactatttatgtccaaatcacggatataacttataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
                                       || ||  |  |  |    |   || | ||  ||   |  | | ||     ||  ||| ||||| || || ||||||||||||||||||||||| || ||||||||||| || ||||| || ||||| || ||||| || ||||||
--------------------------------------gtaagtgaactttccttgaaagcctaacaaaggttgacggtga-tgttccatcg-tttacagGTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAG

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ30517 (Selaginella moellendorffii), 3'ss of exon 4
gtttccaatgttttggaatgtttagaactgatgactatttatgtccaaatcacggatataacttataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
                               |||  | ||   |  ||| | |  | | |  ||   | || |||  | ||       ||   ||| ||||| || || ||||||||||||||||||||||| || ||||||||||| || ||||| || ||||| || ||||| || ||||||
--------------------------gtaagtga--actttccttgaaagc-ctaacaaaggtt--gacagcgatagcaaatgttccatt--gtttacagGTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAG

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|164209876|gb|ES054663.1|ES054663
EST:     GTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAG                         GTTAGAATTGCTCGTATTTTCAACACA
genomic: GTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAGgtaaatattc ... caattttcagGTTAGAATTGCTCGTATTTTCAACACA
EST: gi|124812984|gb|EH897850.1|EH897850
EST:     GTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAG                         GTTAGAATTGCTCGT
genomic: GTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAGgtaaatattc ... caattttcagGTTAGAATTGCTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatcacggatataacttataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
                              ctctaac  putative branch site (score: 2)
                                       cattttc  putative PPT
          atataacttataaga  TA-rich tract