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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtaaataaacaagctagccgccgcatgcatgtgtccccgtgccgtgcagtgtcgcacgtacgtacggccggcctagacgatgacctttgttcgtccaatgtgtgtggtgtggtgtggtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGACCCGGAGCCGTCCAACCCCAAGAAGCGGCGCGACATCGTCCTGTAGAGGA

Basic information

species Zea mays
transcript GRMZM2G340224_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G340224_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g41270.1 (Oryza sativa), 3'ss of exon 7
gtacgtaaataaacaagctagccgccgcatgcatgtgtccccgtgccgtgcagtgtcgcac-gtacgtacggccggcctagacgatgacctttgttcgtccaatgtgtgtggtgtggtgtggtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGACCCGGAGCCGTCCAACCCCAAGAAGCGGCGCGACATCGTCCTGTAGA--GGA-
                       ||||||  |||   | ||    | |  ||     | || | ||        |    | | ||     ||| |       |  ||  | | |||   | || ||||||||||||| ||||||||||||| ||||||| ||| |||||||||||||| ||||||||| ||   ||||| ||||||||||||||| |||| |||||||  ||| 
-------------------gtaagccgcagacat---ttcctacactgctcatccctgaactgaacactgaattgctgaacatgactgaatttctgaacatcac-tgaattgggtgagatcgttcgtgcagGACGGGAGGATCAACTACACGGAGTTCGTGGCCATGATGAGGAAAGGCGACCCGGAGGCG---AACCCGAAGAAGCGGCGCGACGTCGTGCTGTAGATCGGAG
















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|71425328|gb|DR806616.1|DR806616
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
EST: gi|21330641|gb|BQ486022.1|BQ486022
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
EST: gi|71765068|gb|DR963005.1|DR963005
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
EST: gi|7304607|gb|AW600546.1|AW600546
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
EST: gi|86466802|gb|DY233172.1|DY233172
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
EST: gi|21480881|gb|BQ577564.1|BQ577564
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
EST: gi|21390432|gb|BQ528481.1|BQ528481
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGA
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGA
EST: gi|87154477|gb|DY399266.1|DY399266
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
EST: gi|21330105|gb|BQ485486.1|BQ485486
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
EST: gi|21390265|gb|BQ528314.1|BQ528314
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
EST: gi|12046168|gb|BF728307.1|BF728307
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTCGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAT
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
EST: gi|7216885|gb|AW563007.1|AW563007
EST:     TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAAC                         GACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC
genomic: TGGACGGCCGAGACATCAAGGAGATCGTGGCGGAAGTGGACGCCGACAACgtacgtaaat ... gtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtaaataaacaagctagccgccgcatgcatgtgtccccgtgccgtgcagtgtcgcacgtacgtacggccggcctagacgatgacctttgttcgtccaatgtgtgtggtgtggtgtggtgcgtgcagGACGGGCGGATCAACTACACCGAGTTCGCGGCGATGATGAGGAAAGGAGACCCGGAGCCGTCCAACCCCAAGAAGCGGCGCGACATCGTCCTGTAGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA