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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAGgtacttagattcatatatctgtatgtgaataatttgtcttatatagttccataaaactttgaacccaaacatttctaccttcaaatattcgtctcttttcattgcag

Basic information

species Arabidopsis thaliana
transcript AT4G21790.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21790.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA17G01820.1 (Glycine max), 5'ss of exon 8
ATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAGgtacttagattcatatatctgtatgtgaataatttgtcttatatagttccataaaactttgaacccaaacatttctaccttcaaatattcgtctcttttcattgcag-
||| ||||||||||| ||| | ||||| || || || ||||||||||||||||||||| | ||||||     |||    | |  || | |   | ||  ||||||| ||||   ||   | | || |   |  ||| ||   |  | |   | |      | ||||||    
ATTATTTTTCATGCTGAGACGCTTCCCAATTGAATCTAAAGGAAGAAGGAAGAAACTCAATGAGgtatgagcattttcttttaagtgtctatttgata-gtcttat-tagt---atgtcattgtgca---agtcatgtcgtgccactacactactgaaaatctcattgagac
















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|164208734|gb|ES100257.1|ES100257
EST:     GGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAG                         GTTGGATCTGTGACAGCTATATGCTTCACCTGCTTCCTCATAAGATGCGTT
genomic: GGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAGgtacttagat ... ttcattgcagGTTGGATCTGTGACAGCTATATGCTTCACCTGCTTCCTCATAAGATGCGTT
EST: gi|86078543|gb|DR374300.1|DR374300
EST:     TAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAG                         GTTGGATCTGTGACAGCTATATGCTTCACCTGCTTCCTCATAAGATGCGTT
genomic: TAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAGgtacttagat ... ttcattgcagGTTGGATCTGTGACAGCTATATGCTTCACCTGCTTCCTCATAAGATGCGTT
EST: gi|164108788|gb|ES026429.1|ES026429
EST:     TAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAG                         GTTGGATCTGTGACAGCTATATGCTTCACCTGCTTCCTCATAAGATGCG
genomic: TAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAGgtacttagat ... ttcattgcagGTTGGATCTGTGACAGCTATATGCTTCACCTGCTTCCTCATAAGATGCG
EST: gi|125184027|gb|EL198981.1|EL198981
EST:     AAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCAACGAG                         GTTGGATCTGTGACAGCTATA
genomic: AAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCA-CGAGgtacttagat ... ttcattgcagGTTGGATCTGTGACAGCTATA
EST: gi|125013649|gb|EL085918.1|EL085918
EST:     GAGTCAAAAGGAAGAAGGAAGAAACTCCACGAG                         GTTGGATCTGTGACAGCTATATGCTTCACCTGCTTCCTCATAAGATGCGTT
genomic: GAGTCAAAAGGAAGAAGGAAGAAACTCCACGAGgtacttagat ... ttcattgcagGTTGGATCTGTGACAGCTATATGCTTCACCTGCTTCCTCATAAGATGCGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAGgtacttagattcatatatctgtatgtgaataatttgtcttatatagttccataaaactttgaacccaaacatttctaccttcaaatattcgtctcttttcattgcag

- - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA