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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctcttctatttatcacctgtttaatttactctttttaccgaattaaatggttatagcttgcatctagggttctggattttagattttctta...

Basic information

species Arabidopsis thaliana
transcript AT4G27230.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os07g36140.1 (Oryza sativa), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctcttctatttatcacctgtttaatttactctttttaccgaattaaat----ggttatagcttgcatctagggttctggattttagattttctta
  | ||||| || || ||||| ||||| |||||||||||| | || || ||||| || |||||||| ||||||||||| || || ||||||||||||||||||     ||  |||| ||  ||   | | |   ||    ||||| |    | ||||    |      | | ||   ||  |   |||   |   |||||    
CAGGATCGCCCGGTTCTTGAAGGCCGGCAAGTACGCCGAGAGGGTCGGCGCCGGCGCCCCGGTCTACCTCGCCGCCGTCCTCGAGTACCTCGCCGCTGAGgta--tgttcgattctgttcctcctatttcttgattttggtttttgcgcggtgaaatttgggcggggggttcgcggttacagaattgggggtagaattttag--

upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os07g36130.1 (Oryza sativa), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctcttctatttatcacctgtttaatttactctttttaccgaattaa-atggttatagcttgcatctagggttctggattttagattttc--tta
  | |||||  | ||  | || ||||| |||||||||||||| || || ||||| || || ||||| ||||||||||| || || ||||||||||||||||||  | |||  |   ||||      | |||  | |  || |   | | |    |  |  ||   | |    |      |  |  | ||| | |  ||  |||
CAGGATCGCGAGGTTCCTCAAGGCCGGGAAGTACGCCGAGCGCGTCGGCGCCGGGGCCCCCGTCTACCTCGCCGCCGTCCTCGAGTACCTCGCCGCTGAGgtatgc-gtcggtgtgatttggggatttttt--tctgttcgtccgatctaggcgatgttatttcgggtgttgttagatttgtttcagtttggttcgtcgatta

upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os12g25120.1 (Oryza sativa), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctctt--ctatttatcacctgtttaatttactctttttaccgaattaaatggttatagcttgcatctagggttctggattttagattttctta
  | |||||  | ||  | || ||||| |||||||||||||| || || ||||| ||||| ||||| ||||||||||| || || ||||||||||| |||||| ||  ||   |  | |    |   | | ||   |     ||  |  ||| | |  |||  ||      |  |   |  || |  || | |  |   |  
GAGGATCGCCAGGTTCCTCAAGGCCGGCAAGTACGCCGAGCGCGTCGGCGCCGGCGCTCCCGTCTACCTCGCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtattcgctcctgtacccacccgttctcggattggatctgatttgatggcgattgatttggggatctaggtcgccattgtctccgtgttcttggatccgt--

upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os08g33100.1 (Oryza sativa), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctcttctatttatcacctgtttaatttactctttttaccgaattaaatggttatagcttgcatctagggttctggattttagattttctta-
  | ||||| || ||  | || ||||| |||||||||||||| || || ||||| || || ||||| ||||||||||| || || ||||||||||| ||||||    | | |   |         |   ||  |   |   ||  |  | ||   |||  |   |  || || | |  |   |  ||||  ||| ||  | 
CAGGATCGCCCGCTTCCTCAAGGCCGGCAAGTACGCCGAGCGCGTCGGCGCCGGCGCCCCCGTCTACCTCGCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtac---gccacgcatggacgcactcgaattcgtggtcggattggattggat-ggatgaattcgggctgaatttcgtttggggatttttgaattctcgcag

upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G151826_T01 (Zea mays), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgt----aatcagtctcttctatttatcacctgtttaatttactc----------tttttaccgaattaaatggttatagcttgcatctagggttctggattttagattttctta
  | |||||||| ||  | || ||||| |||||||||||||| || || ||||| || || ||||| ||||| || || || || |||||||||||||||||       | || ||   |     | | ||||    ||  ||           |   | |||   ||  ||||| | |||  | |||  ||| |   |               
CAGGATCGCTCGGTTCCTCAAGGCCGGCAAGTACGCCGAGCGCGTGGGCGCCGGCGCCCCTGTCTACCTCGCAGCTGTCCTCGAGTACCTCGCCGCTGAGgttcgtgccccgtttccatttcgccttaactgtggggttcgcttcgggtccctgtcgctgccgtcctatctggttgttgctc-cgtctgcggtgcgacagc-------------

upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA01G02720.1 (Glycine max), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctcttctatttatcacctgtttaatttactctttttaccgaattaaatggttatagcttgcatctagggttctggattttagattttctta----------------------------------
|||||||||  | ||  | || ||||| |||||||||||||| || || |||||||| || ||||| |||||||||||||| ||||| ||||| |||||||||||  |   |   |   | ||   | || | |||  | |||| |   |      |   | ||  | | |||||||||| ||   || |  | |   |                                   
TCGTATCGCCAGGTTCCTCAAGGCCGGAAAGTACGCCGAGCGCGTCGGCGCCGGAGCCCCCGTCTACCTCGCCGCCGTTCTCGAATATCTCGCTGCTGAGgtaatt-gcagcaatttcctgtcgatt-ttcactttgtttttttaaattatcct--tccctgtaattag-atctagggttttgagattcaagtatctgtttttgagtaattgaatgatcggaacattgttttag

upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA12G34360.1 (Glycine max), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctcttctatttatcacctgtttaatttactctttttaccgaattaaatggttata-gcttgcatctagggttctggattttagattttctta------------------------------------
 |||||||| || ||  | || ||||| || ||||| |||||||| || ||||| || || ||||| ||||||||||| || ||||| ||||| |||||||||||      |  | |||  ||     |||    | |  |||| |   |||||  |   |||  | ||  ||||||||||  | | ||| ||||   ||                                     
CCGTATCGCCCGTTTCCTCAAGGCCGGAAAATACGCTGAGCGTGTCGGCGCCGGCGCCCCTGTCTACCTCGCCGCCGTACTCGAATATCTCGCGGCTGAGgtaattg----ccgcaattagtcgttcatttcgaattcgattttga---aattatctccctatgtgattagatctagggtttcgtaatttcgattagattcatttgccctaattgaatggtttgaacattgttttag

upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv19s0014g05020.t01 (Vitis vinifera), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctcttctatttatcacctgtttaatttactctttttaccgaattaaat--ggttatagcttgcatc-----tagggttctg---gattttagattttctta---------
|||||||||||| ||| | |||||||||||||||||||||||||| || ||||| ||||| |||||  | ||||| || || |||||||| ||||| ||||||| |  |||  ||  |  |   |           ||   |      |  ||   |  |||||  | | |  |      ||||||| ||   |||||  || |   ||          
TCGTATCGCTCGTTTTCTCAAAGCCGGTAAGTACGCCGAGCGTGTAGGCGCCGGGGCTCCCGTCTACTTGGCCGCTGTCCTCGAATACCTAGCCGCCGAGgtaaaccatcttctccttaaagttcaccgaagccccacatctagggttgggtttggttcggttagggttagggttagggttagggttatgactgatttgtgactgatttgatgttttag

upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S145_46V6.1 (Physcomitrella patens), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctcttctatttatcacctgtttaatttactctttttaccgaattaaatggttatagcttgcatctagggttctggattttagattttctta--------------------------------------------------------------------------
  | || || || ||||| || || || || ||||||    | ||||| || || ||||| |||||||| |||||||||||||||||| | |||||||||||| |  ||| |||  |||| ||  || |||      | ||   |  |    ||| | | | | ||||   |   || ||| ||   ||  || | | |                                                                           
GAGGATAGCCCGCTTTTTAAAGGCTGGCAAATACGCCACTAGGGTTGGCGCTGGTGCTCCTGTCTATCTTGCCGCCGTTCTTGAATACTTGGCCGCTGAGgtactt-gtcgcttg-atttctccactcttttgccatccctcgatggctctgtaatttgatttggcttcggttgtggtttcgggtggttgaatatacatttcaatccgtcgctgtttccttaatctgtctaggtggatagtctgttcgtttttaactgtcctcttcgtggccag

upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ23553 (Selaginella moellendorffii), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctcttctat-ttatcacctgtttaatttactctttttaccgaattaaatggttatagct----tgcatctagggttctggattttagattt-tctta------------------------------
| | |||||  ||||| | || || || ||||| ||||||||||||||||| ||||| || |||||||||||||| ||||| || ||| | || || ||||| |      |||    | || || |||   || || | ||||||    |  |  |||   |   |||    | | ||   | |||    ||||  ||   || |                               
TAGGATCGCCAGATTTCTCAAGGCGGGCAAGTATGCCGAGCGTGTTGGTGCTGGAGCGCCAGTCTATCTCGCCGCGGTTCTCGAGTACTTGGCGGCAGAGgtgagtgaaatctctcgtgttctcccctccctatttcattcttttccatgtctcgaatcaatcgcgctgaaattcttccctgtttcattcttttgaatcaatcgtgctgattgggtcactccatctccatctccag

upper sequence: AT4G27230.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ34776 (Selaginella moellendorffii), 5'ss of exon 1
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatc--agtctcttctatttatcac-ctgtttaatttactcttttta----ccgaattaaatggttatagcttgcatctagggttctggattttagattt-tctta------------------------------
| | |||||  ||||| | || || || ||||| |||||||| ||||| || ||||| || |||||||||||||| ||||| |||||| | || || ||||| |    | |||||  | ||  || | ||   || || | ||||||      | | | | ||| |   |    | | ||   | |||    ||||  ||   ||                                 
TAGGATCGCCAGATTTCTCAAGGCGGGCAAGTATGCCGAGCGCGTTGGCGCTGGAGCGCCAGTCTATCTCGCCGCGGTTCTCGAATACTTGGCGGCAGAGgtgagtgaaatctctcgtgttcttccctctccctatttcattcttttccatgtctggaatcaatcgcgctgaaattcttccctgtttcattcttttgaatcaatcgcgctgatttggtcactccatctccatctccag

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|86074341|gb|DR370098.1|DR370098
EST:     CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAG                         GTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAAGAAGACCCGTATA
genomic: CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAAGAAGACCCGTATA
EST: gi|86082182|gb|DR377941.1|DR377941
EST:     CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAG                         GTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAAGAAGACCCGTATA
genomic: CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAAGAAGACCCGTATA
EST: gi|164194156|gb|ES118150.1|ES118150
EST:     CTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGG                         GTACTTGAGCTTGCTGGGAACGCAGCAAGAGACAACAAGAAGACCCGTAT
genomic: CTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGA-Ggtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAAGAAGACCCGTAT
EST: gi|86081454|gb|DR377211.1|DR377211
EST:     CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAG                         GTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAAGAAGACCCGTATA
genomic: CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAAGAAGACCCGTATA
EST: gi|164203109|gb|ES094952.1|ES094952
EST:     CTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAG                         GTACTTGAGCTTGCTGGGAACGCAGCAAGAGAACAACAAGAAGACCCGTAT
genomic: CTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAACGCAGCGAGAGA-CAACAAGAAGACCCGTAT
EST: gi|124815847|gb|EH900713.1|EH900713
EST:     CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAG                         GTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAAGAAGACCCGTATA
genomic: CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAAGAAGACCCGTATA
EST: gi|124929017|gb|EL006604.1|EL006604
EST:     CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAG                         GTACTTGAGCTTGCTGGGAAC
genomic: CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAAC
EST: gi|164222251|gb|ES082480.1|ES082480
EST:     CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAG                         GTACTTGAGCTTGCTGGGAACGCAGCAAGAGACAACAAGAA
genomic: CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAAGAA
EST: gi|124807101|gb|EH893560.1|EH893560
EST:     CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAG                         GTACTTGNGCTTGCTGGGAACGCAGCGAGAGA
genomic: CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAACGCAGCGAGAGA
EST: gi|125197053|gb|EL212007.1|EL212007
EST:     TCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAG                         GTACTTGAGCTTGCTGGGAACGCAGCG
genomic: TCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAACGCAGCG
EST: gi|125276909|gb|EL290994.1|EL290994
EST:     CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAG                         GTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAA
genomic: CCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtc ... ctttctatagGTACTTGAGCTTGCTGGGAACGCAGCGAGAGACAACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTATCGCTCGATTTTTGAAAGCCGGTAAGTACGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTATCTCGCCGCCGTTCTTGAATACCTCGCCGCTGAGgtaatcagtctcttctatttatcacctgtttaatttactctttttaccgaattaaatggttatagcttgcatctagggttctggattttagattttctta

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT