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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaattgtttcttcaagtccacaaattgtgaaaacacatcctctgctaacatagtgtgagaacctttcaactgttgcag

Basic information

species Arabidopsis thaliana
transcript AT3G47860.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G47860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os04g53490.1 (Oryza sativa), 5'ss of exon 3
GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaat----tgtt----tcttcaagtccacaaattgtgaaaacacatcctc--tgctaacatagtg-tgagaacctttcaactgttgcag----------
||||||||||||  || | |||||||| |||||||| |||||||| || || || ||||| ||||| ||||| || ||||| |||||||| || ||||||||| |    ||      || |||    || | | |   | | |  |  ||   || |  |  ||   |  | |||| | ||   |               
GAACTTTGACCCAATTCGCTACTCTGGTAGATGGTTCGAAGTAGCATCGCTGAAACGTGGCTTTGCTGGTCAGGGACAAGAGGACTGTCACTGTACTCAGgtattgtagtgccagaatcctcacacacaaatactagtagatcttaatctgtatgatgccccagcaatatgtacctctgaatcctgattcctgaaaacac

upper sequence: AT3G47860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G073743_T03 (Zea mays), 5'ss of exon 3
GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaat-tgtttcttcaagtcc---acaaattgtgaaaacacatcctctgctaacatagtgtgagaacctttcaactgttgcag------------------
 ||||| || || ||| | |||||||| ||||||||||| ||||| ||  | || ||||||||||| ||||| || |||||||||||||| || ||||||||| | |  | | | ||       ||| |||| || |  | |||    || |  ||  |     |   | | ||      ||                   
AAACTTCGATCCAGTTCGCTACTCTGGTAGATGGTTTGAGGTAGCCTCGTTGAAACGTGGATTTGCTGGTCAGGGACAAGAAGACTGTCACTGTACTCAGgtattgtaatacctgaaacatcaaacacattg-gagaggatatctgtagccaggatttttctccattatctaaaaaagaacatctctgtctgtgtgatgat

upper sequence: AT3G47860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G45880.1 (Glycine max), 5'ss of exon 3
GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaattgtttcttcaagt----ccacaaat-tgtgaaaacacatcctctgctaacatagtgtgagaacctttcaactgttgcag----------------
| ||||||||||||| || || || ||||||||||| ||||| ||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||||||| || |     || |    ||  |||| |     |  ||||    |    | |       |  |  |||   || || ||                 
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTCGAAGTTGCTTCACTTAAACGTGGATTTGCAGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagccgtaaatatacaggacaacatttggtatagaaaagagcccattatatttatgctcttccaacatctttccctaatta

upper sequence: AT3G47860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA14G02880.1 (Glycine max), 5'ss of exon 3
GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaattgtttcttcaagtcca----caaat-tgtgaaaacacatcctctgctaacatagtgtgagaacctttcaactgttgcag----------------
| ||||||||||||| || || || ||||||||||||||||| ||||| ||||| ||||||||||| || |||||||||||||||||||||||||||||||||| || |     || |  |     |||| |     |   |||    |    | |       |  |  |||   || || ||                 
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTTGAAGTTGCTTCACTTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagcagtaaatatacaggacggcatttggtttagaaaagagcccattatatttatgctcttccaacatctttccctaatca

upper sequence: AT3G47860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv19s0177g00320.t01 (Vitis vinifera), 5'ss of exon 3
GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaattgtttcttcaagtc---------cacaaattgtgaaaacacatcctctg-----ctaacatagtgtgagaa------cctttcaactgttgcag-
| | |||||||| || || || |||||||||||||||||||||||||| || || ||||||||||| || |||||||||||||| || |||||||||||||||| || |      |||          |   |  || | |     ||||| ||       ||   ||    ||||        | | | || |   |  
GGATTTTGACCCAGTGAGATATTCTGGAAGATGGTTTGAAGTAGCTTCCCTCAAACGTGGATTTGCTGGACAAGGCCAAGAAGATTGCCATTGCACTCAGgtaaatgctgtggacagttatgattggacctgagatgaggatttctatcctttggggcttgaatgcagaaaaagaaatctggtttctgatctctcataat

upper sequence: AT3G47860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ10882 (Selaginella moellendorffii), 5'ss of exon 1
GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaattgtttcttcaagtccacaaattgtgaa---aacacatcctctgctaacatagtgtgagaacctttcaac-tgttgcag
||||||||| || |  |||||  | ||  ||||||||||||| || ||||| ||||| |||||||| || |||||||| ||||| || |||||||| || |||| |     | ||||| | |  ||| |       | ||   ||       ||| |  |      ||   | | |||  |||
GAACTTTGATCCCGCCAGGTATGCCGGTCGATGGTTTGAAGTCGCGTCTCTCAAGCGAGGATTTGCCGGACAAGGCCAGGAAGATTGCCATTGCACACAAgtaagt-----tccaagttctctcattctcgctttgaaactctcttcttcttcatgggcttttcgtctgggatcctgtaacag

upper sequence: AT3G47860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ25927 (Selaginella moellendorffii), 5'ss of exon 1
GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaattgtt---tcttcaagtccacaaattgtgaaaacacatcctctgctaacatagtgtgagaacctttcaactgttgcag
||||||||| || |  |||||  | ||  ||||||||||||| || ||||| ||||| |||||||| || |||||||| ||||| || |||||||| || |||| |      |  ||  || | |   |||   |||| | || ||| ||  ||| |  |    | ||   | |   | |||
GAACTTTGATCCCGCCAGGTATGCCGGTCGATGGTTTGAAGTCGCGTCTCTCAAGCGAGGATTTGCCGGACAAGGCCAGGAAGATTGCCATTGCACACAAgtaagttccaagttctctcgttctcgctttg---aaactc-tcttcttctt-catgggcttttcatctgagatcctgtacag

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|125047725|gb|EL119994.1|EL119994
EST:     TTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGAGTATATACGTTTGA
genomic: TTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaattgttt ... actgttgcagGGAGTATACACGTTTGA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaattgtttcttcaagtccacaaattgtgaaaacacatcctctgctaacatagtgtgagaacctttcaactgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG