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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctattacattttttgtttggtatttatgatttctgtgattgtgtctacatggattaactgttatgattccttaaatctatatttcctgaacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG

Basic information

species Zea mays
transcript GRMZM2G107106_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107106_T06 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 5
--ctctattacattttttgtttggtatttatgatttctgtgattgtgtctacatggatt--aactgttatgattccttaaatctatatttcctgaacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG
  || |   |    ||   ||  || |   |   |  | |  |    |  |    |||   || ||||   | || | |  | || | ||| |  |     |||||| | |||||||| |||||||| || ||||| || ||||||||||||||||
aactgtcgaagggcttcctttaagtgtcctttgatattatagtgtgataaatcacgataggaaatgtttcaactc-tcatttatacaattctttgat---gaagGGCGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAG
















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|32929362|gb|CF034174.1|CF034174
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACGAGGGCTGGCTCATATTCCGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|87157624|gb|DY402413.1|DY402413
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCA-TG                         GGCACAAGGGCTGGCTCATATTC
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTC
EST: gi|71765408|gb|DR963345.1|DR963345
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|71439462|gb|DR820512.1|DR820512
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|74243877|gb|DT651791.1|DT651791
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAAGC-TGC
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAA-GCCTGC
EST: gi|74238077|gb|DT645991.1|DT645991
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|71439479|gb|DR820529.1|DR820529
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|31353283|gb|CD437640.1|CD437640
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCCGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|61119710|gb|DN560671.1|DN560671
EST:     CCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: CCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|32929980|gb|CF034792.1|CF034792
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCCGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|71313388|gb|DR793244.1|DR793244
EST:     CCCATGGCCAGGTATGGGCCAATACTTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: CCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|71313389|gb|DR793245.1|DR793245
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|71446967|gb|DR828017.1|DR828017
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|148947916|gb|EC893413.2|EC893413
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTG
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTG
EST: gi|78115667|gb|DV534055.1|DV534055
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacatggattaactgttatgattccttaaatctatatttcctgaacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG
        gattaac  putative branch site (score: 2)
                           ttaaatctatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctattacattttttgtttggtatttatgatttctgtgattgtgtctacatggattaactgttatgattccttaaatctatatttcctgaacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG