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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAACATAGTCAGCTTGCATGGATATGCCTTGTCTCCTACTGGCAACCTTCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttcttctaactttttttggttcaatttgtgaaagattgatttgcagataaacggtaaaaatgttttgatttttattttcttgaaaag

Basic information

species Arabidopsis thaliana
transcript AT5G62230.2
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G62230.2 (Arabidopsis thaliana), 5'ss of exon 23
lower sequence: GLYMA09G27950.1 (Glycine max), 5'ss of exon 24
AGAAACATAGTCAGCTTGCATGGATATGCCTTGTCTCCTACTGGCAACCTTCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttcttctaacttt----------ttttggttcaatttgtgaaagattgatttgcagata-aacggtaaaaatgttttgatttttattttcttgaaaag
|| ||  | ||||  |||||||| |||||  |  |||||| ||| || ||||||||||||||||| ||||| ||||| || || ||||| ||||||||||||||  |   || || ||           || |  |   ||  ||  | ||  | |      |  ||   ||||||     |  |      |   | |||   
AGGAATCTTGTCACTTTGCATGGTTATGCTCTAACTCCTAATGGAAATCTTCTTTTCTATGACTATATGGAGAATGGCTCTCTGTGGGATCTTCTTCATGgtaatattcactcaccttgaaataactccttggaattttttaatgtgatatgaaatcttgtcttcaataataaaaaaaaaattgtagaaggtgcatcgaa---

upper sequence: AT5G62230.2 (Arabidopsis thaliana), 5'ss of exon 23
lower sequence: GLYMA16G32830.1 (Glycine max), 5'ss of exon 25
AGAAACATAGTCAGCTTGCATGGATATGCCTTGTCTCCTACTGGCAACCTTCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttcttctaactttttttggttcaatttgtgaaagattgatttgcagataaacggtaaaaatgttttgatttttat-tttcttgaaaag---------
|| ||  | ||||  |||||||| |||||  |  |||||| ||| || ||||||||||||||||| ||||| ||||| || || ||||| |||||||||||||  ||||   | |||        ||   || | ||   |   | ||     |||    |       |   |   || | |||  || |  |         
AGGAATCTTGTCACTTTGCATGGTTATGCTCTAACTCCTAATGGAAATCTTCTTTTCTATGACTATATGGAGAATGGCTCTCTGTGGGATCTTCTTCATGgtatattctctaaccttgaaacaactc--cttataaattttcactgtgttatgaaatctcatcttcaataaaaaacttgtatttggtgcacggaaattggaa

upper sequence: AT5G62230.2 (Arabidopsis thaliana), 5'ss of exon 23
lower sequence: GLYMA10G38730.1 (Glycine max), 5'ss of exon 25
AGAAACATAGTCAGCTTGCATGGATATGCCTTGTCTCCTACTGGCAACCTTCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttcttctaact--------ttttttggttcaatttgtgaaagattgatttgcagataaacggtaaaaatgtt--ttgatttttattt-tcttgaaaag------------------------------
|||||  | |||| |||||||||||||||  |  ||||   ||| || ||||||||||||||||| ||||  ||||| ||||| ||||| ||||| ||||||||  |     ||||        | | ||| || |||| ||  | ||||   ||| |  ||   | |  || ||||  || |  | ||| | | ||  |  |                              
AGAAATCTTGTCACCTTGCATGGATATGCTCTTACTCCCTATGGAAATCTTCTTTTCTATGACTATATGGCGAATGGCTCACTGTGGGATCTTCTACATGgtaatgttgctgaactgctagcagtctcttgattgaattagtagatgatt---ttgaaattatttgttgcaagtgttacttcaaatctatatatattacattgttctgatgctgtaattgtcttatgacacag

upper sequence: AT5G62230.2 (Arabidopsis thaliana), 5'ss of exon 23
lower sequence: GLYMA20G29010.1 (Glycine max), 5'ss of exon 20
AGAAACATAGTCAGCTTGCATGGATATGCCTTGTCTCCTACTGGCAACCTTCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttcttctaactttt----tttggttcaatttgtgaaagattgatttgcagataaacggtaaaaa----tgttttgatttttattttcttgaaaag
|||||| | |||| |||||||||||||||  |  ||||   ||| || || |||||||||||||| ||||  ||||| ||||| ||||| ||||| ||||||||  |     ||||  |    |||  || | |   | |     ||||||  | || |   |||  ||    |  ||| | | |  |  | ||  | | 
AGAAACCTTGTCACCTTGCATGGATATGCTCTTACTCCCTATGGAAATCTCCTTTTCTATGACTATATGGCGAATGGCTCACTGTGGGATCTTCTACATGgtaatgttgctcaactgctaggattttcttaattgaattagtagatgattttgaaattatttgtagcaagtgttactttaaatgtggtactttttgacat

upper sequence: AT5G62230.2 (Arabidopsis thaliana), 5'ss of exon 23
lower sequence: Vv16s0022g02030.t01 (Vitis vinifera), 5'ss of exon 24
AGAAACATAGTCAGCTTGCATGGATATGCCTTGTCTCCTACTGGCAACCTTCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttcttctaactttttttggttcaatttgtgaaagattgatttgcagataaacggtaaaaatgttttgatttt-tattttcttgaaaag---------
|||||| | || ||||||||||| ||  |  | || || |  || ||||| || |||||||| |||||||||||||| || || ||||| |||||||| ||| ||||  ||  | |||  ||||     | | ||| | |||   |     | |   | |  || | |||||| ||  ||  |  |  || |          
AGAAACCTTGTTAGCTTGCATGGTTACTCACTATCACCCAAAGGAAACCTGCTCTTCTATGATTACATGGAAAATGGTTCTCTATGGGATCTTCTTCACGgttagttaatc--attttccttggaaatgtatatgataaattatctgatctaaagttgatccaattattttgagttgatacctgttcaaatattttgaaagt

upper sequence: AT5G62230.2 (Arabidopsis thaliana), 5'ss of exon 23
lower sequence: PP1S353_18V6.1 (Physcomitrella patens), 5'ss of exon 23
AGAAACATAGTCAGCTTGCATGGATATGCCTTGTCTCCTACTGGCAACCTTCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaag-----ttcttctaactttttttggttcaatttgtgaaagattgatttgcagataaacggtaaaaatgttttgatttttattttcttgaaaag-------------
 ||||  | ||||   |||  || ||  || ||||  | |  |||||| ||||||||||||| ||||||||||||||     |    || | |||||| |||||      |  | || | | | |    || ||||| | |    || |||| | ||    |  || || | || |  || || |   | || |||              
CGAAATCTTGTCACTCTGCGGGGCTACTCCATGTCCTCCATCGGCAACTTTCTTTTCTATGATTACATGGAAAATGGGAGCTTGCATGATCATCTTCACGgtaaaagccctcatactgaatctgtaaactttaattt-taatttgtttattttccgactg-ctctacaagttttctccttgtt-tcaacgtggaaacctctctgtcgtag

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|164068781|gb|ES119346.1|ES119346
EST:     TCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATG                         GGTCATTGAAGAAAGTGAAGCTTG
genomic: TCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttctt ... tcttgaaaagGGTCATTGAAGAAAGTGAAGCTTG
EST: gi|19878075|gb|AU238906.1|AU238906
EST:     TCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATG                         GGTCATTGAAGAAAGTGAAGCTTGATTGGGAGACAAGGTTGAAGATAGCGG
genomic: TCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttctt ... tcttgaaaagGGTCATTGAAGAAAGTGAAGCTTGATTGGGAGACAAGGTTGAAGATAGCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAACATAGTCAGCTTGCATGGATATGCCTTGTCTCCTACTGGCAACCTTCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttcttctaactttttttggttcaatttgtgaaagattgatttgcagataaacggtaaaaatgttttgatttttattttcttgaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA