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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagggcatatgcttcttttcatagatttagatcaatggcccatttgttttgggtgactggaacgaggaagtgagccttggtttttatggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAG

Basic information

species Zea mays
transcript GRMZM2G409104_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g44140.1 (Oryza sativa), 3'ss of exon 3
gtgagagg-----gcatatgcttcttttcatagatttagatcaatg-gcccatttgttttgggtgactg-gaacgaggaagtgagccttggtttttatggctttgc----agGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTG------GATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAG
|||| |       || |   ||  |  ||    |  |   ||  ||     |||| |   |      |  | || |    | || | ||    |     |  ||||    ||||| ||||||||||||||| |||||||||| || | ||| |||      ||||| || || || ||    || ||||  ||||| ||| |||||||||||      
gtgacaatttcttgcttgcactgatgctcgatcacctgtgtcgctgcaattatttatcaagaactcttatgtactatcttgagatctttctactcacccgtgttgcctgcagGATTCTTGACAACCTTCCTCTGGTCGTCCCGATCAGGAGTTTGTTGGATGATCACGACGCGCCCACATCTTATCAGCTTGGCGTCCATGTCGGCATCAAG------
















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|78110631|gb|DV529039.1|DV529039
EST:     GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACAT                         GATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
genomic: GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
EST: gi|148965278|gb|EE016081.2|EE016081
EST:     GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACAT                         GATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
genomic: GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
EST: gi|89250725|gb|DY622511.1|DY622511
EST:     GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACAT                         GATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
genomic: GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
EST: gi|32793412|gb|CD945648.1|CD945648
EST:     GATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACAT                         GATCCTTGACAACCTTCCTTTGGTCGTCCCAATTA
genomic: GATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTA
EST: gi|101390012|gb|EB816938.1|EB816938
EST:     GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACAT                         GATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
genomic: GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
EST: gi|149013945|gb|EE043446.2|EE043446
EST:     GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACAT                         GATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
genomic: GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
EST: gi|149102922|gb|EE288273.2|EE288273
EST:     GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACAT                         GATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
genomic: GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
EST: gi|149096266|gb|EE181975.2|EE181975
EST:     GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACAT                         GATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
genomic: GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
EST: gi|91871094|gb|EB401239.1|EB401239
EST:     GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACAT                         GATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
genomic: GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
EST: gi|31353543|gb|CD437900.1|CD437900
EST:     GAAGCGATTCATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACAT                         GATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA
genomic: GAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGA

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), 44 (downstream exon)
Score: 120

TGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

TGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

TGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 164

TGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACCGCATAAACATgtgagagggc ... ggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttttgggtgactggaacgaggaagtgagccttggtttttatggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAG
                                      tttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagggcatatgcttcttttcatagatttagatcaatggcccatttgttttgggtgactggaacgaggaagtgagccttggtttttatggctttgcagGATCCTTGACAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG