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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgttatcttggattttgatttccctgtttataataaagaatcattagtaatcgtgagttattgagactcttttattctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGACGATGTACATTTGTTGCCCTTGGAGGCGGTGTGATAGGCGATATGTGTG

Basic information

species Arabidopsis thaliana
transcript AT5G66120.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 2
gtacatgttatcttggattttgatttccctgtt-tataataaagaatcattagtaatcgtgagttattgagactcttt-tattc--tttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGACGATGTACATTTGTTGCCCTTGGAGGCGGTGTGATAGGCGATATGTGTG
    | ||  || ||  |||||| ||  ||||  | |      | |   ||   ||| |    | |   || || | | | |||   |  ||||||||||| ||||||||||| ||||||||||| ||||| || || ||  | || ||||| |||||||| ||||| || |||||||| ||||| |||||||
--gtaggtc-tcatgtgttttgaattggctgtggtgtttgttggcactcttgagaattgca--taagaaagtctttgtgtgttcaactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGGCGGTGTACGTTTGTTGCTCTTGGTGGTGGTGTGATTGGCGACATGTGTG

upper sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G36890.1 (Glycine max), 3'ss of exon 2
gtacatgttatcttggattttgatttccc--tgtttataataaagaatcattagtaatcgtgagttattgagactcttttattc--tttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGACGATGTACATTTGTTGCCCTTGGAGGCGGTGTGATAGGCGATATGTGTG
    ||||  || ||  |||  |||  |   ||||| || |      |  ||   ||| ||     |  | |  |  | | |||   |  ||||||||||| ||||||||||| ||||||||||||||||  || |||||  | || ||||| ||||| || ||||| || |||||||| ||||| |||||||
--gtatgtc-tcatgcgtttgaattggctgttgtttttattggcacttttttgagaattgtataagaaagtg-tttgtgtgttcaactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATTGAGTTGCGACTAGACCGGCGTTGTACGTTTGTCGCTCTTGGTGGTGGTGTGATTGGCGACATGTGTG

upper sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 2
gtacatgttatcttggattttgatttccctgtttataataaagaatcattagtaatcgtgagttattgagactcttttattctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGACGATGTACATTTGTTGCCCTTGGAGGCGGTGTGATAGGCGATATGTGTG
|||   | ||| ||  | ||| | ||  |  ||| |  | ||||     | ||| | |  | | ||| |    |||||||   || ||||| || || |||||||| || |||||||| |||||||| ||  | |||||||| ||||||||||||||| |||| || ||||| || || || |||||||
gta---ggtatattcaagtttcaattaacgatttgtgtttaagatgtgattgtagttgc-attaatttaattgcttttatgtattgtagGACACACTAATGAAAGTTTTTGACAAGGCAATTGAGTCACGGTTGGATAGACGTTGTACATTTGTTGCCGTTGGTGGTGGTGTTATTGGTGACATGTGTG

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|116478278|gb|EG520870.1|EG520870
EST:     TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATG                         GATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
genomic: TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATGgtacatgtta ... ttctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
EST: gi|116421947|gb|EG464539.1|EG464539
EST:     TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATG                         GATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
genomic: TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATGgtacatgtta ... ttctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
EST: gi|116450338|gb|EG492930.1|EG492930
EST:     TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATG                         GATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
genomic: TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATGgtacatgtta ... ttctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
EST: gi|116421951|gb|EG464543.1|EG464543
EST:     TGACAGTGGAAAGTGTAATTTTGCGTGATGGAGAGAAATACAAAGACATG                         GATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
genomic: TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATGgtacatgtta ... ttctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
EST: gi|116421921|gb|EG464513.1|EG464513
EST:     TGATGGAGAGAAATACAAAGACATG                         GATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
genomic: TGATGGAGAGAAATACAAAGACATGgtacatgtta ... ttctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
EST: gi|124948081|gb|EL023871.1|EL023871
EST:     AAATACAAAGACATG                         GATACTCTCATGAAAGTCTTCGACAAGGCCGTTGAGTCTCGCCTAGATAGA
genomic: AAATACAAAGACATGgtacatgtta ... ttctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
EST: gi|116450349|gb|EG492941.1|EG492941
EST:     TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATG                         GATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
genomic: TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATGgtacatgtta ... ttctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
EST: gi|116472855|gb|EG515447.1|EG515447
EST:     TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATG                         GATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
genomic: TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATGgtacatgtta ... ttctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
EST: gi|116421964|gb|EG464556.1|EG464556
EST:     TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATG                         GATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA
genomic: TGACAGTGGAAAGTGTAATTTTGCCTGATGGAGAGAAATACAAAGACATGgtacatgtta ... ttctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataataaagaatcattagtaatcgtgagttattgagactcttttattctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGACGATGTACATTTGTTGCCCTTGGAGGCGGTGTGATAGGCGATATGTGTG
                                     ctcttttattctttct  CT-rich tract
                                        ttttattctttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgttatcttggattttgatttccctgtttataataaagaatcattagtaatcgtgagttattgagactcttttattctttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGACGATGTACATTTGTTGCCCTTGGAGGCGGTGTGATAGGCGATATGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG