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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgccgacaacaccctaaaccaaaattgttttcatgctccgatttggcttacctagaggatggccgctcctacctacgtacgaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTCCCTGAGAGGCAGGCTCTCGAGGAATGGGCAGCAGCCAACAGCAAGGCCG

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 16
gtacgccgacaacaccctaaaccaaaattgttttcatgctccgatttggcttacctagaggatggc-cgctcctacctacgtacgaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTCCCTGAGAGGCAGGCTCTCGAGGAATGGGCAGCAGCCAACAGCAAGGCCG
        |  ||| |  |||| |||| |   |  | |     |      ||   |   |     | | |    |   |  |  |||||   |||| |||||||| || |||||||| ||||| ||||| ||||| |||| ||||||||||| ||||||  | ||||| ||||| |||   |||| |||| | |
------gtatgacaactgaaacaaaaactaagtcaaagtagtaacacattttttttgaggttcaactcaccaagaatcatctttgaatc---agGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTCCCTGAGAAGCAGGCCATTGAGGATTGGGCTGCACAAAACAACAAGACTG
















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|5670866|gb|AI932129.1|AI932129
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCNCCCCTTGTGGCATCG                         GTCTGGGTTTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|211099227|gb|FL470676.1|FL470676
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|7162313|gb|AW519920.1|AW519920
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|4647598|gb|AI622673.1|AI622673
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCNCCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|32909558|gb|CF014370.1|CF014370
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCTGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|148958442|gb|EC904676.2|EC904676
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|60337173|gb|DN204146.1|DN204146
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTATACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|4647597|gb|AI622672.1|AI622672
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|86473157|gb|DY239527.1|DY239527
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|32838972|gb|CD978653.1|CD978653
EST:     AGTTGAGGTCCTGGAAAGGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCTGTGGCTGTC
genomic: AGTTGAGGTCCTGGAAAG-AGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|32836844|gb|CD976522.1|CD976522
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCTGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|20315387|gb|BQ169253.1|BQ169253
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|83279443|gb|DV943451.1|DV943451
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|32837781|gb|CD977459.1|CD977459
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCTGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|32909559|gb|CF014371.1|CF014371
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACCAGCTTCGAGTCGTTCCTCGTTGCTGTGGCTGT
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAAC-AGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGT
EST: gi|4628405|gb|AI619279.1|AI619279
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|13150470|gb|BG320792.1|BG320792
EST:     CAGTTGAGGTCCTGGAAAGAGCATACYTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|148999539|gb|EE036510.2|EE036510
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTTTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|74243995|gb|DT651909.1|DT651909
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|149086278|gb|EE175819.2|EE175819
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|32837912|gb|CD977590.1|CD977590
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCTGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|149098381|gb|EE184357.2|EE184357
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|32867314|gb|CF006996.1|CF006996
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCTGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|78544549|gb|DV622047.1|DV622047
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|149076510|gb|EE165136.2|EE165136
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCGGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|149085815|gb|EE175337.2|EE175337
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTTTGGGTTTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
EST: gi|94479493|gb|EB708451.1|EB708451
EST:     CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCG                         GTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC
genomic: CAGTTGAGGTCCTGGAAAGAGCATACCTGCAGTCACCCCTTGTGGCATCGgtacgccgac ... gaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccgatttggcttacctagaggatggccgctcctacctacgtacgaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTCCCTGAGAGGCAGGCTCTCGAGGAATGGGCAGCAGCCAACAGCAAGGCCG
         ggcttac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgccgacaacaccctaaaccaaaattgttttcatgctccgatttggcttacctagaggatggccgctcctacctacgtacgaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTCCCTGAGAGGCAGGCTCTCGAGGAATGGGCAGCAGCCAACAGCAAGGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG