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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGATATGCTGCGCAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactcttctattttatttctactttctctattcttgatcatggtacctatattctttgttagtgaagtgcatagtttaagttaagttgaggttgcca...

Basic information

species Zea mays
transcript GRMZM2G116034_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116034_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g48750.1 (Oryza sativa), 5'ss of exon 4
GTTTGATATGCTGCGCAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactct-tctattttatttctactttctctattcttgatcatggtacctatattctttgttagtgaagtgcatagttta--agttaagttgaggttgcca
|||||| |||||||| || ||||||||||| |||||| |||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||| | |  | |||   || ||| || |||   | |  ||     |  || |  ||||     ||  |||   ||||  || |  | | |   |    ||    
GTTTGACATGCTGCGTAGGCAGTCCCTCCGTCCTGATTACATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgttagcattatcttagttgtttgtattttgcatttggtttgcggtt-taacactatttagactttctgaga-gcatgattcattaatgattgtacaattctt-
















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|32831294|gb|CD970972.1|CD970972
EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|149057504|gb|EE156642.2|EE156642
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|31363758|gb|CD448115.1|CD448115
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|60338119|gb|DN205092.1|DN205092
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|29544467|gb|CB604847.1|CB604847
EST:     TCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|33095408|gb|CF055402.1|CF055402
EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|31350397|gb|CD434754.1|CD434754
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|149086608|gb|EE176151.2|EE176151
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|148944140|gb|EC889228.2|EC889228
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|148978929|gb|EE026387.2|EE026387
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCC-GCCCAGATTCAGGTTGGA
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGA
EST: gi|78114933|gb|DV533321.1|DV533321
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCANGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|6626380|gb|AW257912.1|AW257912
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|149071683|gb|EE160076.2|EE160076
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATC
EST: gi|67018163|gb|CO446912.1|CO446912
EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|31349869|gb|CD434226.1|CD434226
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|32837445|gb|CD977123.1|CD977123
EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|6626315|gb|AW257847.1|AW257847
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCACGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|31363551|gb|CD447908.1|CD447908
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATC
EST: gi|31354925|gb|CD439282.1|CD439282
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|31355862|gb|CD440219.1|CD440219
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|31360434|gb|CD444791.1|CD444791
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|32846950|gb|CD986631.1|CD986631
EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|30705620|gb|CD058849.1|CD058849
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|71768076|gb|DR966013.1|DR966013
EST:     TGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGGTTTCA-GGATCAG                         ATTTACGACATCTTCCAGCT
genomic: TGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGG-TTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCT
EST: gi|148953344|gb|EE152835.2|EE152835
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCNAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|211294752|gb|FL286232.1|FL286232
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCCAGGATCAG                         ATTTACGACATCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTC
EST: gi|149023519|gb|EE045864.2|EE045864
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCCAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|149097051|gb|EE182858.2|EE182858
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCCAGCTTCTCCCAGCCCAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTC
EST: gi|60346532|gb|DN213505.1|DN213505
EST:     TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTACGACATCTTCC
genomic: TTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCC

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), 46 (downstream exon)
Score: 177

GTTTGATATGCTGCGCAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTCTCTGCTACCATGCCCCCTGAGGCCCTTGAGATTACCCGCAAGTTCATGA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 176

GTTTGATATGCTGCGCAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTCTCTGCTACCATGCCCCCTGAGGCCCTTGAGATTACCCGCAAGTTCATGA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 172

GTTTGATATGCTGCGCAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTCTCTGCTACCATGCCCCCTGAGGCCCTTGAGATTACCCGCAAGTTCATGA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 61

GTTTGATATGCTGCGCAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactctt ... tgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTCTCTGCTACCATGCCCCCTGAGGCCCTTGAGATTACCCGCAAGTTCATGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGATATGCTGCGCAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTAGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaactcttctattttatttctactttctctattcttgatcatggtacctatattctttgttagtgaagtgcatagtttaagttaagttgaggttgcca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT