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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgcccttaaatctctcatcgagcaagttcattcatattcacaatgcccatgtctatatggagtgtttttttatttcctctttcatag

Basic information

species Zea mays
transcript GRMZM2G069827_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069827_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g01350.2 (Oryza sativa), 5'ss of exon 1
------GTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgta---atgcccttaaatctctcatcgagcaagttcattcatat--tcacaatgcccatg---tctatatggagtgtttttttatttcctctttcatag---------
      |||||| || || ||||||||| | |||||||| ||||| |||||||||||||| |  || ||||||||||||||||| || ||||||||||| |||   |   |   | || | |   |   |  |||  ||| ||   || | ||| | |||   | |    | |   || |||| |||  |  || || |         
TTCAAGGTACGAAGAACAGCGCAACATGCTCTACAACCAGACCTATAATCTCGACCAAGTCGCTTTCGCTGCCGATGGCCTCAAAGACGCTCAGCAGACCgtacgtactactccacatatatagcccgccttgtttgttcctactgtctccatgtctatgaattattgccgaaccattcttttgtttgttaatttatcgattcctcag

upper sequence: GRMZM2G069827_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g01350.1 (Oryza sativa), 5'ss of exon 3
GTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgta---atgcccttaaatctctcatcgagcaagttcattcatatt--cacaatgcccatg---tctatatggagtgtttttttatttcctctttcatag---------
|||||| || || ||||||||| | |||||||| ||||| |||||||||||||| |  || ||||||||||||||||| || ||||||||||| |||   |   |   | || | |   |   |  |||  ||| || |  | | ||| | |||   | |    | |   || |||| |||  |  || || |         
GTACGAAGAACAGCGCAACATGCTCTACAACCAGACCTATAATCTCGACCAAGTCGCTTTCGCTGCCGATGGCCTCAAAGACGCTCAGCAGACCgtacgtactactccacatatatagcccgccttgtttgttcctactgtctccatgtctatgaattattgccgaaccattcttttgtttgttaatttatcgattcctcag
















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|211462348|gb|FK983889.1|FK983889
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAA
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAA
EST: gi|5608282|gb|AI901949.1|AI901949
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
EST: gi|21432410|gb|BQ547900.1|BQ547900
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
EST: gi|211462343|gb|FK983884.1|FK983884
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
EST: gi|60354422|gb|DN221395.1|DN221395
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
EST: gi|211462347|gb|FK983888.1|FK983888
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCA
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCA
EST: gi|4646509|gb|AI491649.2|AI491649
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
EST: gi|76915903|gb|DV166159.1|DV166159
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
EST: gi|211257952|gb|FL452751.1|FL452751
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
EST: gi|21432431|gb|BQ547921.1|BQ547921
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
EST: gi|8665725|gb|BE186541.1|BE186541
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
EST: gi|71775453|gb|DR973331.1|DR973331
EST:     TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT                         ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT
genomic: TCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgccct ... tctttcatagATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACTgtaatgcccttaaatctctcatcgagcaagttcattcatattcacaatgcccatgtctatatggagtgtttttttatttcctctttcatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG