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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcatcatcatatctttaaagtatatctcttagtgtgaatgcattttttccttcactgcaaatgtatcttacttctccttcgccgtggttacacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATCCGGATACAAGTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGA

Basic information

species Zea mays
transcript GRMZM2G057408_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057408_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g45840.1 (Oryza sativa), 3'ss of exon 5
-cgcatcatcat--atctttaaagtatatctcttagtgtgaatgcattttttccttcactgcaaatgtatcttacttctccttcgccgtggttacacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATCCGGATACAAGTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGA
    |||||  |  |  | | || |||  ||    ||  |  |   |  |||  | ||||  |    |||   | || |  | | |  |||||||||||||||| |||||||||||||| |||||||||| ||| |||||||||||||||||||| ||||| ||||||||||||||||  ||||| |||||||||||| ||||
ttatatcatatttaaattgttaaatattccttgaggtaggcttcagtgctttattccactatattcttat---aattttgttcctctctggttacacatgcagCTATGCCAGATTTTGCACAAGTATACAGCTTTCTGGGAAGCATATTTGATCCAGATACTAGTGGGCATTTGCAGACTTTAAAGGCGATGGATCCAATTGA
















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|78076508|gb|DV504942.1|DV504942
EST:     GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTG                         CCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAA
genomic: GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTGgtgagcactt ... acacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAA
EST: gi|71428976|gb|DR810026.1|DR810026
EST:     GAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTG                         CCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATC
genomic: GAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTGgtgagcactt ... acacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATC
EST: gi|78118281|gb|DV536668.1|DV536668
EST:     GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTG                         CCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATC
genomic: GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTGgtgagcactt ... acacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATC
EST: gi|148956892|gb|EC902815.2|EC902815
EST:     GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTG                         CCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAA
genomic: GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTGgtgagcactt ... acacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAA
EST: gi|60397572|gb|DN230388.1|DN230388
EST:     GTCGAGCAAGAAAATATGGTTCCACCACTCCGTG                         CCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATC
genomic: GTCGAGCAAGAAAATATGGTTCCACCACTCCGTGgtgagcactt ... acacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATC
EST: gi|110220916|gb|EC902814.1|EC902814
EST:     CCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTTCCCCCACTCCGTG                         CCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGGAAGCATATTTGAT
genomic: CCAACTTCTGAAGCAGTCGAGCAAGAAAATATGG-TTCCACCACTCCGTGgtgagcactt ... acacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCT-GGGAAGCATATTTGAT
EST: gi|91876492|gb|EB406449.1|EB406449
EST:     GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCCTG                         CCATGCCAGATTT
genomic: GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTGgtgagcactt ... acacatgcagCCATGCCAGATTT
EST: gi|71763063|gb|DR961000.1|DR961000
EST:     GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTG                         CCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATC
genomic: GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTGgtgagcactt ... acacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATC
EST: gi|78118283|gb|DV536669.1|DV536669
EST:     GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTG                         CCATGCCAGATTTTGCCCCAGTATACTACTTCCTGGGAAGCATATTTGATC
genomic: GCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACTCCGTGgtgagcactt ... acacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccttcactgcaaatgtatcttacttctccttcgccgtggttacacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATCCGGATACAAGTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGA
                    atcttac  putative branch site (score: 3)
              aaatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgcatcatcatatctttaaagtatatctcttagtgtgaatgcattttttccttcactgcaaatgtatcttacttctccttcgccgtggttacacatgcagCCATGCCAGATTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATCCGGATACAAGTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - -tgaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -cactgca