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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtctttagcattagacttgtttacatgttttcccttgatgaatcgctgtttgtttgagttatgaaacgctcagttataaactagttagaaataata...

Basic information

species Zea mays
transcript GRMZM2G127453_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127453_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g56890.1 (Oryza sativa), 5'ss of exon 3
GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtctttagcattagacttgtttacatgtt-ttcccttgatgaatcgctgtttgtttgagttatgaaacgctcagttataaa-ctagttagaaataata-
|| |||||| |||||||||| ||||||||||| |||||||||||||||||||||||||| |||||||| || |  |   ||| | || ||| |  |  |||| |||  |||  |   | |  || ||||||  ||| ||   ||       ||  | ||       |  || 
GTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAACTACATTCCATGAAAAAGgtaatgca--agcttgaggctt-tccatctgttgttctgttgcagctgcacgattggtttgaagtataaagtacttgaaaccaactcaagccttgtgtgctag
















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|32936461|gb|CF041280.1|CF041280
EST:     GCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: GCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|31909649|gb|CD651024.1|CD651024
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|211042955|gb|FK963033.1|FK963033
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACTAGTAA
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|211042961|gb|FK963039.1|FK963039
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|113667155|gb|DW831402.1|DW831402
EST:     CCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAAGTA
genomic: CCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAA-GTA
EST: gi|211167601|gb|FL258650.1|FL258650
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGGCAAACAAGTA
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGG-CAAACAAGTA
EST: gi|211245830|gb|FL313150.1|FL313150
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|31353639|gb|CD437996.1|CD437996
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|211042950|gb|FK963028.1|FK963028
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGT
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGT
EST: gi|32870084|gb|CF009766.1|CF009766
EST:     AACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: AACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|211156223|gb|FL476869.1|FL476869
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|211167597|gb|FL258646.1|FL258646
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTA
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTA
EST: gi|78180798|gb|DV551171.1|DV551171
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|8665358|gb|BE186174.1|BE186174
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|211167599|gb|FL258648.1|FL258648
EST:     ATATGAAGTTCCTAGATCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTA
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTA
EST: gi|211045919|gb|FK963047.1|FK963047
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|8401369|gb|BE057003.1|BE057003
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|5525193|gb|AI861191.1|AI861191
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|211104453|gb|FL478968.1|FL478968
EST:     ATATGAAGTTCCTAGATCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|88755570|gb|DY539711.1|DY539711
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAA
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|31909179|gb|CD650789.1|CD650789
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|211167596|gb|FL258645.1|FL258645
EST:     ATATGAAGTTCCTAGATCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|166465671|gb|EG323069.1|EG323069
EST:     CGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: CGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
EST: gi|31360970|gb|CD445327.1|CD445327
EST:     ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA                         TTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG
genomic: ATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 165

GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAGGCACATGGCACATCAGTTCCGCCCAATACAGCTGTTGTTGTATCCACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 826

GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAGGCACATGGCACATCAGTTCCGCCCAATACAGCTGTTGTTGTATCCACCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 471

GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAGGCACATGGCACATCAGTTCCGCCCAATACAGCTGTTGTTGTATCCACCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 470

GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtcttt ... aattttgcagTTCATGGACAAATCGTGCAGTGTTATGGACTCATCTATGGCAAACAAGTAGGCACATGGCACATCAGTTCCGCCCAATACAGCTGTTGTTGTATCCACCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAgtgagtctttagcattagacttgtttacatgttttcccttgatgaatcgctgtttgtttgagttatgaaacgctcagttataaactagttagaaataata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaataa