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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGACCAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcgtggtttcagtttctgctcttttatttaaatatccttgtctcgtgaagattgtgtttcatgaaaattttctgaactattctacag

Basic information

species Arabidopsis thaliana
transcript AT1G75380.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75380.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 5
GCAAGACCAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcgtggtttcagtttctgctc-ttttatttaaatatccttgtctcgtgaagattgtgtttcatgaaaattttctgaactattctacag----------------------
|||||||||||||| |||||||| |||||||| ||| | || ||||||||||| || ||| | ||  | |    ||| | |  |  || | |||   ||    |   ||    | |||||    |      ||||  | |    ||| |                         
GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggttactagaaatagtctatagtagttgtgtttggttacaaataagtc----aaattgtaccactcattcatttatttattccttccatcattgtgtttgattttggttccag

upper sequence: AT1G75380.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA14G07830.1 (Glycine max), 5'ss of exon 5
GCAAGACCAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcgtggtttcagtttctgctcttttatttaa--atatccttgtctcgtgaagatt-gtgtttcatgaaaattttctgaactattctacag------------------
|| ||||| ||  |||||||||| |||||||| ||| | |||||||||||||||||||||   |||   ||||   ||| | |||||     |||   |||  |  |||    |  |||   ||| || ||  |  ||  |||  |    |                     
GCTAGACCTACTTTGTATCAAGTAGTGAAGGAGATGATTGACAAGATGGGTTACGAAgtaaaattct--gtttatctttatactcttactcctaattgtattgtcatctttccatcattcaggttccacgatgaaattaagaatcaaatcatgttgtttcctgcttccacag

upper sequence: AT1G75380.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA1784S00200.1 (Glycine max), 5'ss of exon 4
GCAAGACCAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcgtggtttcagtttctgctcttttatttaaatatcct----tgtctcgtgaagatt-gtgtttcatgaaaattttctgaactattctacag------------------
|| ||||| ||  |||||||||| |||||||| ||| | ||||||||||||||||||||| | |||   ||||   ||| | |||||     ||| | |  |    | | |    |  |||   ||| || ||  |  ||  |||  |    |                     
GCTAGACCTACTTTGTATCAAGTAGTGAAGGAGATGATTGACAAGATGGGTTACGAAgtaagattct--gtttatctttatactcttactcctaattgtgttgtgatatttttccatcattcaggttccacgatgaaattaagaatcaaatcatgttgtttcatgcttccacag

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|124775721|gb|EH865850.1|EH865850
EST:     ATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
genomic: ATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
EST: gi|124996261|gb|EL068530.1|EL068530
EST:     CCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
genomic: CCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
EST: gi|125046952|gb|EL119221.1|EL119221
EST:     ACCATGTATCAAGTGGTGAAGGAAATGGTGGAACAAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACC
genomic: ACCATGTATCAAGTGGTGAAGGAAATGGTGGA-CAA-GATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACC
EST: gi|124864013|gb|EH948450.1|EH948450
EST:     CAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTT
genomic: CAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTT
EST: gi|124955850|gb|EL030827.1|EL030827
EST:     GGTGGACAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
genomic: GGTGGACAAGATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
EST: gi|47829045|gb|CK118729.1|CK118729
EST:     CAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
genomic: CAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGACCAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcgtggtttcagtttctgctcttttatttaaatatccttgtctcgtgaagattgtgtttcatgaaaattttctgaactattctacag

- - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - AAGATG