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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaattgtgaaacttttgcttgcatctgtgtttattctctcattactggatatttctctagactttcttgctgcttatagtgaacaaaaacctcttgcagGACTTGTCTGGTCGACCATATCTTGGTTACAACTTGGAGATACCAACTCAGAGAGTTGGAACATATGATACTCAG

Basic information

species Arabidopsis thaliana
transcript AT3G22425.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G22425.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G39370.1 (Glycine max), 3'ss of exon 4
gtataaaattgtgaaacttttgcttgcatctgtgtttattc-tctcattactggatatttctctagactttcttgctgcttatagtgaacaaaaacctcttgcagGACTTGTCTGGTCGACCATATCTTGGTTACAACTTGGAGATACCAACTCAGAGAGTTGGAACATATGATACTCAG
     | ||  |     || || |    | |  ||  |    |   ||| ||     ||||||   |||| | |  ||  |     | |||   || | || ||||| |||||||| |||||| ||||  |||| || ||||| ||||| |||||||| ||||| |||||||||||||||
----gagatctttctctttctgttcattttttagtcaagcaataaaatttctcttattttctcgctacttccctcatgggttcctcgcacacttacatttt-cagGATTTGTCTGGCCGACCACATCTAAGTTATAATTTGGACATACCCACTCAGAGGGTTGGGACATATGATACTCAG

upper sequence: AT3G22425.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G28420.2 (Glycine max), 3'ss of exon 4
gtataaaattgtgaaacttttgcttgcatctgtgtttattc-tctcattactggatatttctctagactttcttgctgcttatagtgaacaaaaacctcttgcagGACTTGTCTGGTCGACCATATCTTGGTTACAACTTGGAGATACCAACTCAGAGAGTTGGAACATATGATACTCAG
     | ||  |     || || |    | |  ||  |    |   ||| ||     |||||||  |||| |||  ||  |     | |||   || | || ||||| |||||||| |||||| ||||  |||| || ||||| ||||| |||||||| ||||| |||||||||||||||
----gagatctttctctttctgttcattttttagtcaagcaataaaatttctcttattttctctctacttccttcatgggttcctcgcacacttacttttt-cagGATTTGTCTGGCCGACCACATCTAAGTTATAATTTGGACATACCCACTCAGAGGGTTGGGACATATGATACTCAG
















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|164123799|gb|ES163979.1|ES163979
EST:     TAGATGAAGCGCTTATACATGTTTCCTTG                         GACTTGTCTGGTCGACCATATCTTGGTTACAACTTGGAGATACCAACTCAG
genomic: TAGATGAAGCGCTTATACATGTTTCCTTGgtataaaatt ... cctcttgcagGACTTGTCTGGTCGACCATATCTTGGTTACAACTTGGAGATACCAACTCAG
EST: gi|86080767|gb|DR376524.1|DR376524
EST:     TCACAGCTCCTCTAGATGAAGCGCTTATACATGTTTCCTTG                         GACTTGTCTGGTCGACCATATCTTGGTTACAACTTGGAGATACCAACTCAG
genomic: TCACAGCTCCTCTAGATGAAGCGCTTATACATGTTTCCTTGgtataaaatt ... cctcttgcagGACTTGTCTGGTCGACCATATCTTGGTTACAACTTGGAGATACCAACTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggatatttctctagactttcttgctgcttatagtgaacaaaaacctcttgcagGACTTGTCTGGTCGACCATATCTTGGTTACAACTTGGAGATACCAACTCAGAGAGTTGGAACATATGATACTCAG
                                             cctcttgc  CT-rich tract
                                     aacaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaaattgtgaaacttttgcttgcatctgtgtttattctctcattactggatatttctctagactttcttgctgcttatagtgaacaaaaacctcttgcagGACTTGTCTGGTCGACCATATCTTGGTTACAACTTGGAGATACCAACTCAGAGAGTTGGAACATATGATACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT