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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTCCGCGCCGACGTCCGTGCTGCCGGACTACGCCAAGAAGGCCGTGCCCGACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagcgccatccgcggtcgcgagctgtcttccctcaaaattgcttcttcccccgcagcttgagatgctcgatggagctgggacgtggtagtacct...

Basic information

species Zea mays
transcript GRMZM5G821024_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G821024_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g06170.1 (Oryza sativa), 5'ss of exon 1
AGTCCGCGCCGACGTCCGTGCTGCCGGACTACGCCAAGAAGGCCGTGCCCGACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagcgccatccgcggtcgcgagctgtcttccctcaaaattgc-ttcttcccccgcagcttgagatgctcgatggagctgggacgtggtagtacct
 || || |     ||||| || ||| |||||||||||||||||| |||||| ||| |||||||||||||||||||||||||||||||||||||| ||||||| || |       |         ||   |   |        |  ||  || ||       |   | |||       |    |    || |     || | 
TGTTCGAGGGCGAGTCCGCGCCGCCCGACTACGCCAAGAAGGCCATGCCCGCCGATAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCGAAGAGgtcagaattttttttttcacactacggtttcagtagaaatggagctggattttttaaaaaaaaaattagaaaagaagtttttcaacaacttttctttagc-
















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|149078521|gb|EE167303.2|EE167303
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|71443975|gb|DR825025.1|DR825025
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|71432288|gb|DR813338.1|DR813338
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|76020990|gb|DT948160.1|DT948160
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCCAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGA
EST: gi|76291030|gb|DV030598.1|DV030598
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|74233755|gb|DT641669.1|DT641669
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|74235022|gb|DT642936.1|DT642936
EST:     CCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: CCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|76017161|gb|DT944331.1|DT944331
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|76291031|gb|DV030599.1|DV030599
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|50327405|gb|CO522531.1|CO522531
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCG
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCG
EST: gi|71427971|gb|DR809021.1|DR809021
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|78121824|gb|DV540208.1|DV540208
EST:     CCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: CCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|50330894|gb|CO526020.1|CO526020
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|71427972|gb|DR809022.1|DR809022
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|50330895|gb|CO526021.1|CO526021
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|76289897|gb|DV029465.1|DV029465
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|78121825|gb|DV540209.1|DV540209
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|50334050|gb|CO529176.1|CO529176
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAG
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAG
EST: gi|93282762|gb|EB675026.1|EB675026
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|71440800|gb|DR821850.1|DR821850
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|71760728|gb|DR958665.1|DR958665
EST:     ACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: ACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|74233756|gb|DT641670.1|DT641670
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|78084547|gb|DV512940.1|DV512940
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCCAGCGCGCCAAGAG                         GATCCTGGCGAATCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|74235023|gb|DT642937.1|DT642937
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|71763915|gb|DR961852.1|DR961852
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|148946272|gb|EC891573.2|EC891573
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCT
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCT
EST: gi|76921491|gb|DV168604.1|DV168604
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCCAGGAGAGGAAGATCAA
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAA
EST: gi|71322705|gb|DR798033.1|DR798033
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAG
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAG
EST: gi|50336682|gb|CO531808.1|CO531808
EST:     GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAG                         GATCCTGGCGAACCGGCAGTCTGCGGCGAG
genomic: GACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 45

AGTCCGCGCCGACGTCCGTGCTGCCGGACTACGCCAAGAAGGCCGTGCCCGACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCC


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 63

AGTCCGCGCCGACGTCCGTGCTGCCGGACTACGCCAAGAAGGCCGTGCCCGACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

AGTCCGCGCCGACGTCCGTGCTGCCGGACTACGCCAAGAAGGCCGTGCCCGACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 72

AGTCCGCGCCGACGTCCGTGCTGCCGGACTACGCCAAGAAGGCCGTGCCCGACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagc ... cgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCCGCGCCGACGTCCGTGCTGCCGGACTACGCCAAGAAGGCCGTGCCCGACGACAGGCTCGCCGAGCTCGCGCTCCTCGACCCCAAGCGCGCCAAGAGgtaagcaagcgccatccgcggtcgcgagctgtcttccctcaaaattgcttcttcccccgcagcttgagatgctcgatggagctgggacgtggtagtacct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC