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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttctttatatgctttgtgattggaagaaggagatttcagtgtgtgtactaactgcaccaatactatgtgatgtctgaaactggttcctgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT

Basic information

species Arabidopsis thaliana
transcript AT4G32760.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 1
-attttctttatatgctttgtgattggaagaaggagatttcagtgtgtgtactaactgcaccaatactatgtgatgtctgaaactggttcctgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT
 |  |  ||  |    |||   |||    | |      | | || | ||| ||   |  | | |   |   | ||   ||||  |||||    |||   ||||||||||| ||||| || |||||||| ||||| || ||||| || | ||||||||||| ||| ||||||||  | || 
aacctctttgttgcaatttactattatggggaaattcatactgtatttgtgctg-ttcaatctagggtgaataattcttgaatatggttttgatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAATCCAAAAGTTCAACTTCTTGCACTGACG
















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|47828022|gb|CK117706.1|CK117706
EST:     GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGC                         GCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA
genomic: GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGCgtatgtttcc ... tgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA
EST: gi|86063774|gb|DR359531.1|DR359531
EST:     GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGC                         GCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA
genomic: GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGCgtatgtttcc ... tgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA
EST: gi|125089272|gb|EL147703.1|EL147703
EST:     GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGC                         GCAAGCAAAAGATGTTGTGAAAGGCATT
genomic: GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGCgtatgtttcc ... tgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATT
EST: gi|86063771|gb|DR359528.1|DR359528
EST:     GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGC                         GCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAW
genomic: GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGCgtatgtttcc ... tgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA
EST: gi|86063772|gb|DR359529.1|DR359529
EST:     GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGC                         GCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA
genomic: GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGCgtatgtttcc ... tgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA
EST: gi|86063777|gb|DR359534.1|DR359534
EST:     GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGC                         GCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA
genomic: GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGCgtatgtttcc ... tgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA
EST: gi|86063778|gb|DR359535.1|DR359535
EST:     GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGC                         GCAAN-AAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA
genomic: GATTGGGCTATGAACCTCGAGATCTGTGATATGCTCAATAGCGATCCAGCgtatgtttcc ... tgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtactaactgcaccaatactatgtgatgtctgaaactggttcctgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT
   tactaac  putative branch site (score: 0)
                                         ttcctgtttt  putative PPT
                aatactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttctttatatgctttgtgattggaagaaggagatttcagtgtgtgtactaactgcaccaatactatgtgatgtctgaaactggttcctgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT