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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtttatactatataatggtaaaacttatttgcagagtttgcatggcagtattgcatgttcaggtaattcaccttgttttctgcaattattattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA

Basic information

species Zea mays
transcript GRMZM5G877316_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G877316_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g21990.1 (Oryza sativa), 3'ss of exon 2
-catgtttatactatataatggtaaaacttatttgcagagtttgcatggcagtattgcatgttcaggtaa--ttcaccttgttttctgcaattat-tattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA
   |||  || |    || ||    || || |  ||    ||||||    | |||   ||  | |||  |  || |   | |||| ||  ||  | || |||||||||  |||||||||||||||||| ||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
ttgtgtcaattcatagtattgtgtgaagttttcagctttctttgca----actatcatatagtaaggctatcttaatgattttttttgttatgctatactgcagAGGCCAGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGCTGGA

upper sequence: GRMZM5G877316_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 2
catgtttatactatataatggtaaaacttatttgcagagtttgcatggca-gtattgcatgttcaggtaattcac-cttgttttctgca-attattattgc-agAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA
    ||| ||   |||        | ||||| |       ||   |  || ||||      || | ||  |   | ||| | || ||   ||    ||  | || ||||||||||||||||||||||| || || ||||| || ||  ||||||||||| ||||||| |||||| | |||||||||||| ||||||||| ||| 
---ttttgtaggctattgcatgtgagcttatattattgtgttatttatcatgtatgtttaatttatgttgtgggcacttatcttttgtttatctccatccccaGTGGCACGCGGATTAAGACCCGCAAACGAAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGG-

upper sequence: GRMZM5G877316_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 2
catgtt-tatactatataatggtaaaacttatt--tgcagagtttg-catggcagtat--tgcatgttcaggtaattcacctt-gttttctgcaattattattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA
 || || ||  ||||   ||| ||     ||||  ||     |||  ||||   ||||  |  ||||| |||   ||  | || ||||    ||||        ||| ||||||||||||||||||||||| ||||| ||||| || ||  ||||||||||| ||||||| |||||| | |||||||||||| ||||||||| ||| 
-attttgtaggctattgcatg-tagcttctattattgtgttatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccc-----cagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT

upper sequence: GRMZM5G877316_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 2
catgtttatactatataatggtaaaacttatttgcagagtttg--catggcagtattgcatgtt-caggtaattcaccttgttttctgcaattattatt--------gcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA
               || || ||   ||| |||      |||    | | ||   ||  |||||    | | |||    | |  |  | |  |||| ||        ||||||| |||||||||||||||||||| ||||| ||||| |||||| ||||||||||| | || ||||||||| | ||||||||||| |  ||||||| ||| 
-------------gttagtgatacctcttctttttgagtttttactaggacaaattttgatgttgttagcatttctttgtatacttagaagctattcttatgtacgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT

upper sequence: GRMZM5G877316_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 2
catgtttatactatataatggtaaaacttat-ttgcagagtttgcatggcagtattgcatgttcaggtaattcaccttgt---tttctgca-attattat-tgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA
      | | || ||   || |  | ||| | ||  | | | |  |    || |||   | ||    | |||    || |   ||| ||   ||| |||| || ||||| ||||||||||||||||||||  |||| ||||| |||||| | ||||||||  | || ||||||||| | || ||||||||||||||||||| ||| 
-----ctcttctttaagttgtttcatcttttgttagaaattgttaacatgagcattaagt-ttagaatgattgtaattataagtttgtgtttatttttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT

upper sequence: GRMZM5G877316_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 3
catgtttatacta--tataatggtaaaacttatttgca-gagtttgcatggcagtattgcatgttcaggtaattcaccttgttttctgcaattattattg--cagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA
   ||  | | ||  || | | |  ||  || ||  |  | ||||   |      |||   |||| |  |||  |   ||||  | ||    |||| ||   ||| ||||||||||||||||||||||| ||||| |||||||| ||  ||||||||||| ||||  | |||||| | |||||||||||||||||||||| ||| 
-tggtggaaagtaactacagtagcgaacattcttgacgtgtgtttttgttatcaaatt---tgttgacataagcc-tgttgtcatttgtttctatttttttccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCAGCGCCGCTGGACCCTGCAACATTTGCAGATGCAGTGGTCCAGATTTATCTGGATAATGCTGGT

upper sequence: GRMZM5G877316_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ06557 (Selaginella moellendorffii), 3'ss of exon 2
catgtttatactatataatggtaaaacttatttgcagagtttgcatggcagtattgcatgttcaggtaattcaccttgttttctgcaattattattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA
                    ||||    |  |||      |||||| |   | | |  || |  |||  ||   | || |||  ||   |||      || ||||||||||||||||||||||| ||||| ||||||  ||| ||||||||  | || ||| | ||||| || |||||||| ||  ||||| ||| ||| 
--------------------gtaagggct--ttgagattcttgcattg-gttttggtttggtttggt--ttgttcatgatttgggcgtgtat------agTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCAATTCCGTTGGACCCATCTTCTTTCGCGGATGCTATAGTCCAGATCTACTTGGATCATGCTGGT

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|18662176|gb|BM501785.1|BM501785
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|50331541|gb|CO526667.1|CO526667
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|78108789|gb|DV527206.1|DV527206
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|76912266|gb|DV164646.1|DV164646
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|61117466|gb|DN558427.1|DN558427
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|71428140|gb|DR809190.1|DR809190
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|19436862|gb|BM953272.1|BM953272
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|211134644|gb|FL028665.1|FL028665
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|76287488|gb|DV027056.1|DV027056
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|19057519|gb|BM736186.1|BM736186
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|87153853|gb|DY398642.1|DY398642
EST:     ATGAGCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: ATGAGCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|19057686|gb|BM736353.1|BM736353
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|19436861|gb|BM953271.1|BM953271
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|78084791|gb|DV513184.1|DV513184
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
EST: gi|78084825|gb|DV513218.1|DV513218
EST:     GCTCGAAGGAGAAGCCCACTCTTGG                         AGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC
genomic: GCTCGAAGGAGAAGCCCACTCTTGGgtaagactct ... attattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcagtattgcatgttcaggtaattcaccttgttttctgcaattattattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA
                                         aattattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtttatactatataatggtaaaacttatttgcagagtttgcatggcagtattgcatgttcaggtaattcaccttgttttctgcaattattattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA