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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcgtgtgtgtacaagccactgatgcgaaaaaactgttggtgtggaagtttatgatacttgaagctgtattttagacacatttttcttcttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAAGCTGAGCGCTAAGCTTATCTTTGGCGCTGACAGGTATTCTCTGTTTGAC

Basic information

species Zea mays
transcript GRMZM2G094712_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094712_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 3
tctcgtgtgtgtacaagccactgatgcgaaaaaactgttggtgtgg-aagtttatga---tacttgaagctgtattttagacacatttttcttcttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAAGCTGAGCGCTAAGCTTATCTTTGGCGCTGACAGGTATTCTCTGTTTGAC
     || || |||| |      |  | |   |    ||  |   | ||  ||||||   || |   || |||||||||       || | | ||| |  ||||||||||||| ||||||||  | || ||||| || ||||| || |||||||||||||| ||||||||||| ||||| ||||||||                
---gatgggtttacaggaagaaaaaaccattgactattttttacagcaaacttatgatgatattcccagttgtattttacctgtgattatttgctt-tgactagGTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG----------------

upper sequence: GRMZM2G094712_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g03770.t01 (Vitis vinifera), 3'ss of exon 3
tctcgtgtgtgtacaagccactgatgcgaaaaaactgttggtgtggaagtttatgatacttgaagctgtattttagacacatttttcttcttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAAGCTGAGCGCTAAGCTTATCTTTGGCGCTGACAGGTATTCTCTGTTTGAC
    ||| |  | | |  || |         |   |     ||||||||        | ||| ||      || ||   || ||| | |   |||   ||||| || ||||| || || || || ||    || ||||| |||||||||||  |||| |||||||| || ||||||||||||||                
----gtgaggattcta-tcattttcattgtgatggtaactttgtggaag--------aattggagta----ttgagcttcaatttccatggcattc--agGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAAATTGAGTGCTAAGCTCATGTTTGGCGCTGACAG----------------
















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|67021032|gb|CO449781.1|CO449781
EST:     GCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCC                         GTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAA
genomic: GCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCCgtaagtgtca ... ttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAA
EST: gi|18385028|gb|BM418227.1|BM418227
EST:     CTAGTGCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCC                         GTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAA
genomic: CTAGTGCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCCgtaagtgtca ... ttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAA
EST: gi|211351968|gb|FL217074.1|FL217074
EST:     CTAGTGCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCC                         GTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAA
genomic: CTAGTGCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCCgtaagtgtca ... ttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAA
EST: gi|61119383|gb|DN560344.1|DN560344
EST:     CTAGTGCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCC                         GTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCT
genomic: CTAGTGCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCCgtaagtgtca ... ttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCT
EST: gi|18385008|gb|BM418207.1|BM418207
EST:     CTAGTGCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCC                         GTCACGTGTCAAGGAGTACCTACCA-TCACCGGTCTGGCTGAATTCA-TAA
genomic: CTAGTGCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCCgtaagtgtca ... ttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtttatgatacttgaagctgtattttagacacatttttcttcttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAAGCTGAGCGCTAAGCTTATCTTTGGCGCTGACAGGTATTCTCTGTTTGAC
                                cacatttttcttctta  CT-rich tract
                                   atttttcttcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcgtgtgtgtacaagccactgatgcgaaaaaactgttggtgtggaagtttatgatacttgaagctgtattttagacacatttttcttcttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAAGCTGAGCGCTAAGCTTATCTTTGGCGCTGACAGGTATTCTCTGTTTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA