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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgtttag

Basic information

species Arabidopsis thaliana
transcript AT3G23990.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 13
ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttag-tccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattg---tgtttag-------
||||| || |||||||| || ||||| || ||||||||||||||||| || || ||  ||||||| |||||||| ||||||||||| ||  | ||||| || | ||   ||| ||||||    |   | || |  |||        |   |||    |||     |  |||    | ||  |      | |         
ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTACAGGAGCGGTTGGCAAAGCTCTCCGGAGGTGTTGCTGTTCTAAAGgtgaggttcacaatattatgttt----atattgaggaatatatattgaatgaaataacaaactttccgaacattccatggttagataaaccatctgaaagagcc

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 12
ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccat-gttataatgt-----tttgggagtcttagaatcatagcagcctggttgtaagtgtc-ttgttataact----tctggagctaattg-tgtttag---------------------------------
||||| |||||| ||||    ||||| |||||||||||||||||||| || || ||| ||||||| |||||||||||||||||||| ||  ||||||| ||   || |   || |||     |||  || |  |||| | | |    | || ||   |  ||  |||| ||||||     |||  |||   || | |||                                   
ATTAGATCAGCAGTTGAGAACAGCACTTCAGATTATGACAAGGAAAAGCTCCAGGAACGGTTGGCAAAGCTCTCTGGAGGTGTTGCTGTTCTGAAGgtgaggttattgacctactgtatgtatttacgaatggtaga-ttacatgttcttgttttatatcgtaattgtaataactgttacctgtggctctctgatatttcctgattttgtgcctatgtgtgcatcctttcctag

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G111477_T02 (Zea mays), 5'ss of exon 1
----ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttc--tggagctaattgtgtttag----------------------------------------
    ||||| |||||||||||    ||||| ||||||||||| |||||||| || || ||  ||||||| || ||||||||||||||||| ||  ||||||| ||      |||      ||||   || |   |||   ||   ||  |||  ||   | || ||     |    |   | ||  ||||| |                                          
GTTGATTAGATCAGCAATTGAGAATAGCACTTCAGATTATGATAAGGAAAAGCTCCAGGAGCGGTTGGCAAAACTCTCTGGAGGTGTTGCTGTTCTGAAGgtgag-----attactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctag

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 13
ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccatgttataatgttttggg-agtcttagaatcatagcagcctggttgtaagtgtcttgttat---------aacttctggagctaattgtgtttag
||||||||||||||||||   || |||||||||||||||||||||||  | || ||||| || || ||||| ||||| |||||||||||| | |||||  | | |  || |    ||||||  | |  |  |  | | |    |           ||  ||  ||          || | |  | ||     | |  ||
ATTAGGTCAGCAATTGAAAACAGTACCTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCAGTGCTTAAGgtatgcctac-ttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgcaatggaaaaattgacatttaaaactgcccttttgcag

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 13
ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccatgttataatgttttgggag-tcttagaatcatagcag---cctggttgtaag----tgtcttgtta----taacttctggagctaattgtgtttag
||||| ||||||||||||   ||||| ||||||||||||||||||||  | || ||||| || || ||||| ||||| |||||||||||  |||||||| ||  || | |   |   |||   | | |||| ||  || | |   | |  |  || |    |||| || ||    |||| |||| | |      | |  ||
ATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAGgtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcag

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA10G33680.1 (Glycine max), 5'ss of exon 13
ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccatgttataatgttttgggagtcttagaatcatagca---gcctggttgtaag----tgtcttgtta----taacttctggagctaattgtgtttag
||||| ||||||||||||   ||||| ||||||||||||||||||||  | || ||||| || || ||||| ||||| |||||||||||  |||||||| ||  || | |   |   |||   |   |  | || || |    || |  |  || |    |||| || ||    |||| |||| | |      | |  ||
ATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAGgtttgtttatttgagtttaccttgcttgctgttaagtcttatctggtgcttcatcatatggttttgtcatgataaaattaacatctgaaaccttacttttgcag

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 13
ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccatgttataatgttttgggagtcttagaatcatagc-agcctggttgtaagtgtcttgttataacttc-tggagctaattgtgtttag--------
|||||||| |||||||||   ||||||||||||||||||||||||||  | || ||||| || || ||||| ||||| |||||||| ||| | |||||  | | |  |||     ||||||  ||    || | ||  |  || | ||||| | |  |  |  ||| |     |||||    |      |         
ATTAGGTCTGCAATTGAAAACAGCACCTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCCGTGCTTAAGgtatgcctac-ttacgtcattttggttgttaatgatttatccctggcatagttgtcaatacc--ggcatagcggaacggagcggcctaccccaaaaatgagat

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 13
ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagt-ccatgttataatgttttgggagt----cttagaatcatagcagc-ctggttgtaagtgtcttgttataacttctggagctaattgtgtttag----------------------------------------------
||||||||||| |||||| ||||||| || |||||||||||||||||  |||||||||||||||| ||||| ||||| |||||||| || ||||||||  ||  ||  ||| ||         | |      |||  |  | |  || ||      | | |      ||    | ||     | || | |  |                                                
ATTAGGTCAGCCATTGAATTGAGCACTTCTGATTATGACAAGGAAAAGTTGCAAGAAAGGTTGGCCAAGCTTTCTGGTGGTGTTGCTGTCTTGAAGgtctgtatcaatttacaaatccccaacattactgtctaggcttgttgaggctctaaactcaggagctactgtactggtactcagattcatggggaatgttatctagatatatataaaaatggtggaaaattgcttccctttgcag

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ32351 (Selaginella moellendorffii), 5'ss of exon 11
ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgtttag
|| ||   |||  |  |    ||||| ||||| |||||||||||||| || ||||||||| |||| ||||||||||||||||| || || ||||||||  || ||    | | | || ||| ||  ||   || || |      |   |  || ||                                 
ATCAGAGAAGCTGTGAAGTCTAGCACATCAGACTATGACAAGGAAAAGCTCCAAGAAAGGCTGGCCAAGCTCTCTGGAGGTGTAGCCGTCTTGAAGgtatgtacaccaaagacttttgtggcagcgtttttattattgt--ttcgcgcgcgagcgtag-------------------------------

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ20894 (Selaginella moellendorffii), 5'ss of exon 11
ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgtttag
|| ||   |||  |  |    ||||| ||||| |||||||||||||| || ||||||||| |||| ||||||||||||||||| || || ||||||||  || |     | | | || ||| ||  ||   || || |      |   |  |||||                                 
ATCAGAGAAGCTGTGAAGTCTAGCACATCAGACTATGACAAGGAAAAGCTCCAAGAAAGGCTGGCCAAGCTCTCTGGAGGTGTAGCCGTCTTGAAGgtacgtacgccaaagacttttgtggcagcgtttttattattgt--ttcgcgcgcgagtgtag-------------------------------

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|124764522|gb|EH854652.1|EH854652
EST:     CTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAG                         ATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAAGACAGAGTGAC
genomic: CTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccat ... ttgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAA-GACAGAGTGAC




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG