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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgaagaaaatgaacactacatttattatggttcaatatccatgttatatataaactgaatgcttgtgtttaattggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCGGCTGATGAGATGGCTGTTGAGGAACCTACTGAAATCATCGGAGCTTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G04840.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G28780.2 (Glycine max), 3'ss of exon 4
--gtgagtgaagaaaatgaacactacatttattatggttcaata-------tccatgtt--atatataaactgaatgcttgtg---tttaattggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCGGCTGATGAGATGGCTGTTGAGGAACCTACTGAAATCATCGGAGCTTAAG---
   |  || ||     |  | |  |||| | | |    | |||         |||||||   |  ||    |  |||| | ||   |||  |   |||||||||| |||||||||||||   | ||||||||||  ||||||||||| || |||||||| || |  |  |||||||| ||||||||  | ||||||| |    
tgattggtcaatcttttccaaataacatgtctcacaaataaatgatgtgctcccatgtttggtggattggtttgatgcctctgctttttggtccttgtagGTTCATGGAGATTACTCAG---AGGATGTTGGTGCCAAGGTAGACAGACCTGCTGATGAAATAGTGGCAGAGGAACCCACTGAAATTGTTGGAGCTTGATTTC
















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|116436618|gb|EG479210.1|EG479210
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
EST: gi|125317190|gb|EL331275.1|EL331275
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGC
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGC
EST: gi|124862592|gb|EH947029.1|EH947029
EST:     CCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
genomic: CCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
EST: gi|164158452|gb|ES060169.1|ES060169
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGC
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGC
EST: gi|86081250|gb|DR377007.1|DR377007
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
EST: gi|163976997|gb|EL996686.1|EL996686
EST:     GATCCTCAAGGCCCCCCAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
genomic: GATCCTCAAGG-CCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
EST: gi|125083331|gb|EL143928.1|EL143928
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGA
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGA
EST: gi|164155410|gb|ES038406.1|ES038406
EST:     GATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGA
genomic: GATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGA
EST: gi|86077074|gb|DR372831.1|DR372831
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
EST: gi|164175420|gb|ES126669.1|ES126669
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGA
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGA
EST: gi|116436720|gb|EG479312.1|EG479312
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
EST: gi|125285576|gb|EL299661.1|EL299661
EST:     CGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
genomic: CGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
EST: gi|125084935|gb|EL144968.1|EL144968
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGA
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGA
EST: gi|125105225|gb|EL159055.1|EL159055
EST:     AGGCCCCTAAATTCGACCCTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
genomic: AGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
EST: gi|125028154|gb|EL100423.1|EL100423
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCAACGGAAGATTACTCAGCAGAAGATGTTGG
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCA-CGGA-GATTACTCAGCAGAAGATGTTGG
EST: gi|164219816|gb|ES072510.1|ES072510
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCC
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCC
EST: gi|124835964|gb|EH920403.1|EH920403
EST:     CCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
genomic: CCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCG
EST: gi|125200559|gb|EL215513.1|EL215513
EST:     AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAG
genomic: AAGTCAAGATCCTCAAGGCCCCTAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAG
EST: gi|124944352|gb|EL020460.1|EL020460
EST:     AGTCAAGATCCTCAAGGCCCCTTAAATTCGACCTTGGCAAGCTCATGGAT                         GTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGA
genomic: AGTCAAGATCCTCAAGGCCCC-TAAATTCGACCTTGGCAAGCTCATGGATgtgagtgaag ... attggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttcaatatccatgttatatataaactgaatgcttgtgtttaattggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCGGCTGATGAGATGGCTGTTGAGGAACCTACTGAAATCATCGGAGCTTAAG
                                        gtttaat  putative branch site (score: 4)
       aatatccatgttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgaagaaaatgaacactacatttattatggttcaatatccatgttatatataaactgaatgcttgtgtttaattggtgtagGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACAGGCCGGCTGATGAGATGGCTGTTGAGGAACCTACTGAAATCATCGGAGCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT