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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacacactgatgatacataatgtgtcgacaaggctattgcatctcttttttcacttgaacttctcatccttaatattgcaatggtatatttgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG

Basic information

species Arabidopsis thaliana
transcript AT2G31610.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 3
-aacacactg-atgatacataatgtg-tcgacaaggcta--ttgcatctcttttttcacttgaacttctcatccttaatattgcaatggtatatttgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG
 || |   || |   |  |  ||||  || |||||  |   |||  ||||||| |  | ||  | || |        | |||    || | | | |  |   |||||| || ||||||||  | || ||||||||||||||||| |||||||| ||||||                                             
aaatagcttgtactgtttaggatgttctctacaagcatgctttgtttctctttatgtattttgatttttgtctgactaaatt----tgttgtttcttttgc-cagGGCGTGCTATGGTGTGCTCAGGTTTGTTATGGAGAGTGGTGCTAAGGGCTGTGAG---------------------------------------------

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 3
aacacactgatgatacataatgtgtcgacaaggcta--ttgcatctcttttttcacttgaact-tctcatccttaat--attgcaatggtatatttgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG
     | || |   | ||  | ||||   | |      |||     ||| |||  | |   || | |  || || ||  | |  | || | | || ||| | |||||| |||||||||||| | || ||||| ||||||||||| |||||||| ||||||                                             
----aattgttaggatatcct-tgtcagtatgctccatttgttcaccttgtttttcctctgctatgtagtcttttatttactaaactgttttgttcgattttcagGGCATGTTATGGTGTTCTCAGGTTTGTCATGGAGAGTGGTGCTAAGGGCTGTGAG---------------------------------------------

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G26890.1 (Glycine max), 3'ss of exon 3
aacacactgatgatacataatgtgtcgacaaggctattgcatctcttttttcacttgaacttctcatc---cttaatattgcaatg-gtatatttgatata-cagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG
     |||  | ||  |  |  |           | || |  |  ||     | |   | || ||       ||    || |  || ||| | ||  | |  ||||||||| |||||||||||||| ||||||||||||||||| ||||||||||| |||                                             
-----actagtaattgaacaaatactattgttcttttttccccctttgcacgaatgttatttttctgtgggtttgtgtttactttgtgtaaactttctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG---------------------------------------------

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G26790.1 (Glycine max), 3'ss of exon 3
aacacactgatgatacataatgtgtcgacaaggctattgcatctcttttttcacttgaacttctcatc--cttaatattgcaatg-gtatatttgatata-cagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG
     |||  | ||  |  || |           | |  |  |  |      |  |||  ||    |    ||    || |  || ||| | ||  | |  ||||||||| |||||||||||||| ||||||||||||||||| ||||||||||| |||                                             
----aactagtaattgaacatatactattgttcttttcccccccttgcacgaatgtgatttttctgtgggtttgtgtttactttgtgtaaacttcctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG---------------------------------------------

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G21190.1 (Glycine max), 3'ss of exon 3
--aacacactgatgatacataatgtgtcgacaaggctattgcatctcttttttcacttgaacttctcatccttaatattgcaa--tggtatatttgatata-cagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG
  ||| | |||     |  |  | | |   |        || ||    || ||    ||   || |  |     | ||||||   || |  | ||  | |  |||||| || |||||||| ||||| ||||||||||||||||| ||||||||||| |||                                             
ctaaccctctgtattgatgtccttttttccccctttccatgaatgcaattctt-gtgtgggtttgtagt----gacattgcagactgttgaactttctgtttcagGGCTTGCTATGGTGTCTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG---------------------------------------------

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G33230.1 (Glycine max), 3'ss of exon 3
---aacacactgatgatacataatgtgtcgacaaggctattgcatctcttttttcacttgaacttctcatccttaatattgcaatggtatatttgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG
          |  |  |  | ||| | |  |  |    | | | |||   ||        ||  |   |  ||  ||||  |  |    |||||| |   |||||| || ||||||||||| |||||||| ||||| ||||| || ||||| ||||||                                             
tcttttctcttttttttttaaaatttttttatgaatacaattcttctgcattgctgtggcaaaattataatctctatatatct-taaactatttgttt--cagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGTGGTGCCAAGGGTTGTGAG---------------------------------------------

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0016g01380.t01 (Vitis vinifera), 3'ss of exon 3
aacacactgatgatacataatgtg-tcgacaaggctattgcatctcttttt-tcacttgaacttctcatccttaatattgcaa-tggtatatttgatatac-agGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG
     | || | | || |       |   ||| |    |   || |  | | |  | ||    |   | || |||| |  |   ||||   | |  |||   |||||||| |||||||||||||||||  ||||||| ||||| || ||||||||||||                                             
----aagtgttaacacttgccacacttagcaatgtggattagtcacgatctgtttcatggctgttcgagccctaatttgccttctggttgctgtcctattttagGGCCTGCTATGGTGTTTTGAGATTCATTATGGAAAGTGGGGCAAAGGGATGTGAG---------------------------------------------

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|164136494|gb|ES040974.1|ES040974
EST:     GCTTCTCGGTGGTCTTGCTGTTCGCAG                         GGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATG
genomic: GCTTCTCGGTGGTCTTGCTGTTCGCAGgtacgacatt ... tgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATG
EST: gi|116442865|gb|EG485457.1|EG485457
EST:     CAGGCTGAGTCTCTACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAG                         GGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATG
genomic: CAGGCTGAGTCTCTACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAGgtacgacatt ... tgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATG
EST: gi|125033264|gb|EL105533.1|EL105533
EST:     CAGGCTGAGTCTCTACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAG                         GGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAG
genomic: CAGGCTGAGTCTCTACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAGgtacgacatt ... tgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAG
EST: gi|164127452|gb|ES010384.1|ES010384
EST:     TACAAGCTTCTCGGTGGTCTTGCTGTTCGCAG                         GGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGC
genomic: TACAAGCTTCTCGGTGGTCTTGCTGTTCGCAGgtacgacatt ... tgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGC
EST: gi|86080151|gb|DR375908.1|DR375908
EST:     GCTGAGTCTCTACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAG                         GGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGGAGCTAAGGGAT
genomic: GCTGAGTCTCTACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAGgtacgacatt ... tgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGG-AGCTAAGGGAT
EST: gi|116410815|gb|EG453407.1|EG453407
EST:     CAGGCTGAGTCTCTACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAG                         GGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATG
genomic: CAGGCTGAGTCTCTACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAGgtacgacatt ... tgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATG
EST: gi|125075829|gb|EL139224.1|EL139224
EST:     TACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAG                         GGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATG
genomic: TACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAGgtacgacatt ... tgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATG
EST: gi|124751029|gb|EH841159.1|EH841159
EST:     CAGGCTGAGTCTCTACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAG                         GGCCTGTTATGGTGTTTTGAG
genomic: CAGGCTGAGTCTCTACGTTACAAGCTTCTCGGTGGTCTTGCTGTTCGCAGgtacgacatt ... tgatatacagGGCCTGTTATGGTGTTTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcacttgaacttctcatccttaatattgcaatggtatatttgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG
                                       tatatttgatataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacacactgatgatacataatgtgtcgacaaggctattgcatctcttttttcacttgaacttctcatccttaatattgcaatggtatatttgatatacagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
aacacac
- - - - - - - acataat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctca