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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGCCCTCTGGGGAAAGCTAGCAGCAGAAATCCTAATGCAGAACTGGGATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccatcaatgtttcgtagtgtgttctttgctctttgtatatgttatattagtaaccttgttccttccttatcttttggcag

Basic information

species Zea mays
transcript GRMZM2G038313_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038313_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G33770.1 (Glycine max), 5'ss of exon 3
GAGTGCCCTCTGGGGAAAGCTAGCAGCAGAAATCCTAATGCAGAACTGGGATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctacc---------atcaatgtttcgta-----gtgtgttctttgctctttgtatatgtt------atattagtaaccttgttcctt---ccttatcttttggcag----------------------
||||||  | ||||| ||||| ||||| |||||  | ||||||||||||||  | ||| | || ||  |||| |||||||||||||| ||||||||||||||| | |           |  || ||| |       |  |||||||   | |  ||  || ||      | ||   |   ||||||  ||   | | || | ||   |                       
GAGTGCATTGTGGGGGAAGCTGGCAGCTGAAATTTTGATGCAGAACTGGGACATTGCTCTTGAAGAGCTCAATCGCTTGAAGGAAATCATTGATTCAAAGgttgttcttgtttgtcagttgatctttggagtagatgcatgttcttgtttgtcagttgatctttggagtagatgcatgttcttgtttgttatgcttaatatattaatatagactggtgaacttcgttgcag

upper sequence: GRMZM2G038313_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G16090.1 (Glycine max), 5'ss of exon 3
GAGTGCCCTCTGGGGAAAGCTAGCAGCAGAAATCCTAATGCAGAACTGGGATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctacc-----atcaatg---tttcgtagtgtgt-----tctttgctctttgtatatgttatattagtaaccttgttccttccttatcttt-tggcag
||||||  | ||||| ||||| ||||| |||||  | ||||||||||||||  | ||| | || ||  ||||||||||||||||||| ||||| ||||||||| | |       ||| |     || | |||   |     |  ||| |  ||||   |   |||||  |||  | |     |  | | |||| | ||||
GAGTGCATTGTGGGGGAAGCTGGCAGCTGAAATTTTGATGCAGAACTGGGACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatt--taatatagactggtggtgaactttgttgcag
















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|71333152|gb|DR803610.1|DR803610
EST:     ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|67042197|gb|CO468452.1|CO468452
EST:     ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|149075427|gb|EE163945.2|EE163945
EST:     ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|71438188|gb|DR819238.1|DR819238
EST:     ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|149070764|gb|EE159177.2|EE159177
EST:     ATGTGGCTTTGGAGGAATTCA-CCGCTTGAAGGAGATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|148996096|gb|EE035357.2|EE035357
EST:     ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|32844599|gb|CD984280.1|CD984280
EST:     ATGTGGCATTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|71429761|gb|DR810811.1|DR810811
EST:     ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|149077453|gb|EE166147.2|EE166147
EST:     ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAA
genomic: ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAA
EST: gi|71318808|gb|DR796165.1|DR796165
EST:     ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT

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: 548

GAGTGCCCTCTGGGGAAAGCTAGCAGCAGAAATCCTAATGCAGAACTGGGATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 342

GAGTGCCCTCTGGGGAAAGCTAGCAGCAGAAATCCTAATGCAGAACTGGGATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 322

GAGTGCCCTCTGGGGAAAGCTAGCAGCAGAAATCCTAATGCAGAACTGGGATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 356

GAGTGCCCTCTGGGGAAAGCTAGCAGCAGAAATCCTAATGCAGAACTGGGATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccat ... cttttggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGCCCTCTGGGGAAAGCTAGCAGCAGAAATCCTAATGCAGAACTGGGATGTGGCTTTGGAGGAATTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaccatcaatgtttcgtagtgtgttctttgctctttgtatatgttatattagtaaccttgttccttccttatcttttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA