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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCTGTGCCCGGAGCCGTACCCAGAGACGAACACGGAGTTCCTCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaacttggtttcaacgaaatcctctgctgcttcgtggttggttagccatagttcatggaggcgtagaattactttggatggattaaaatatgg...

Basic information

species Zea mays
transcript GRMZM2G134389_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134389_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g10650.1 (Oryza sativa), 5'ss of exon 2
GTACCTGTGCCCGGAGCCGTACCCAGAGACGAACACGGAGTTCCTCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaacttggtttcaacgaaatcctctgctgcttcgtggttggttagccatagttcatggaggcgtagaattactttggatggattaaaatatgg-----
|||||||||||||||||||||||| ||||||||| ||||||||||||  ||||||||||||| ||||||||||||||||||||||||||| |||||||   |||| |||    ||  || |    |  |  ||||| ||   ||  | ||  ||  | ||  | || ||   |  |  |||  ||  ||||  |     
GTACCTGTGCCCGGAGCCGTACCCGGAGACGAACGCGGAGTTCCTCGCCAAGAACGGGATCAAGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaacgaaacatgg----aaaaaatttgagttatctttcgttgtcaattc-cgattcttactagaatcatataaaaccggttcatgttttccaataacgtatcg
















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|211385283|gb|FL301230.1|FL301230
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTC
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTC
EST: gi|211509867|gb|FL433772.1|FL433772
EST:     AACGGGATCAGGCTCCACCAGCTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: AACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|211387917|gb|FL301248.1|FL301248
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAG
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAG
EST: gi|5555286|gb|AI881237.1|AI881237
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|5555280|gb|AI881231.1|AI881231
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|211385286|gb|FL301233.1|FL301233
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCCGATGACAAAATA
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCC-GATGACAAAATA
EST: gi|5555378|gb|AI881329.1|AI881329
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|93281321|gb|EB673585.1|EB673585
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|211387907|gb|FL301238.1|FL301238
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTC
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTC
EST: gi|50339825|gb|CO534951.1|CO534951
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|211385282|gb|FL301229.1|FL301229
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAAC-ATTTGTCAATATACCCGATGA
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGA
EST: gi|32845463|gb|CD985144.1|CD985144
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|211387914|gb|FL301245.1|FL301245
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGC
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGC
EST: gi|78087468|gb|DV515861.1|DV515861
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|211387912|gb|FL301243.1|FL301243
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAAT
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAAT
EST: gi|76294316|gb|DV033884.1|DV033884
EST:     TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAG                         GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTT

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: 45 (upstream exon), 49 (downstream exon)
Score: 55

GTACCTGTGCCCGGAGCCGTACCCAGAGACGAACACGGAGTTCCTCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GTACCTGTGCCCGGAGCCGTACCCAGAGACGAACACGGAGTTCCTCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

GTACCTGTGCCCGGAGCCGTACCCAGAGACGAACACGGAGTTCCTCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 51

GTACCTGTGCCCGGAGCCGTACCCAGAGACGAACACGGAGTTCCTCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaa ... ttttctgcagGAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCTGTGCCCGGAGCCGTACCCAGAGACGAACACGGAGTTCCTCGAGAAGAACGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGAAAGgtaagaaaaacttggtttcaacgaaatcctctgctgcttcgtggttggttagccatagttcatggaggcgtagaattactttggatggattaaaatatgg

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