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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgtgttgacagtctaggcgtcctctccaccattgcgctgatggttgcttattaggtatgtcatgatgtgctttcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT

Basic information

species Zea mays
transcript GRMZM2G081682_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 18
---------------gtaaatgtgttgacagtctaggcgtcctctc--caccattgcgctgatggttgcttatt---aggtatgtcatgatgtgctttc-ctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCA---TGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT-
                || | |  || |   ||   |  |  |      | | ||| | ||||| ||||| |||   |  | ||   | ||||| |||| |  | ||||||||||| ||||||||||||||  |||| ||||||||| ||  |      ||| ||||| || ||||||||      |  |||| |     | | ||| | | 
gtaactggaattataatatacgcatttaacttcatagtataatagaaatatctttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGCTGTTCATAGTTCTAGGAATAAAGCCTAGCACGCCTTT----GGAAACGGAATG
















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|33101487|gb|CF061447.1|CF061447
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|6466763|gb|AW191423.1|AW191423
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|32908733|gb|CF013546.1|CF013546
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGGGGGAGATTCTGTTCCAGTCTGTCCTATAGAATGATGGTGCCAT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACT-GGCGGAGATTCTGTTCCAGTCTGCCCTATAG-ATGATGGTGCCAT
EST: gi|5762062|gb|AI967110.1|AI967110
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|24764290|gb|CA399456.1|CA399456
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|5739589|gb|AI947384.1|AI947384
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|211046951|gb|FL455967.1|FL455967
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAGCAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATG--G-TGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|6095640|gb|AW120307.1|AW120307
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGCCCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|4688570|gb|AI637240.1|AI637240
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAAATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|26559536|gb|CA831771.1|CA831771
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|9794851|gb|BE553159.1|BE553159
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|32916469|gb|CF021281.1|CF021281
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|60347665|gb|DN214638.1|DN214638
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTCCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|87155905|gb|DY400694.1|DY400694
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|211046948|gb|FL455964.1|FL455964
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAGCAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATG--G-TGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|7145170|gb|AW506651.1|AW506651
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|21389890|gb|BQ527939.1|BQ527939
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|211046950|gb|FL455966.1|FL455966
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAGCAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATG--G-TGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|32866939|gb|CF006621.1|CF006621
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|166552970|gb|EG247183.1|EG247183
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTC
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTC
EST: gi|74232803|gb|DT640717.1|DT640717
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|60358930|gb|DN225903.1|DN225903
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|22715090|gb|BU197572.1|BU197572
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|22715088|gb|BU197571.1|BU197571
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCCGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|60398484|gb|DN231300.1|DN231300
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|32909378|gb|CF014190.1|CF014190
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|31250143|gb|CD219167.1|CD219167
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAAATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|16926966|gb|BM080034.1|BM080034
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|21331635|gb|BQ487016.1|BQ487016
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|76014001|gb|DT941171.1|DT941171
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|166450987|gb|EG077507.1|EG077507
EST:     AAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATACCGGTCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCC
genomic: AAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCAT-CCGG-CAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCC
EST: gi|5804468|gb|AI979438.1|AI979438
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|74237144|gb|DT645058.1|DT645058
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|60350641|gb|DN217614.1|DN217614
EST:     GGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: GGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattgcgctgatggttgcttattaggtatgtcatgatgtgctttcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT
       cgctgat  putative branch site (score: 4)
                                        tgctttcct  putative PPT
                    ttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgtgttgacagtctaggcgtcctctccaccattgcgctgatggttgcttattaggtatgtcatgatgtgctttcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC