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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttctaacaaccaagaaccttgtaagtgacattgcaagcggttccgatgttgctctgatgttgcagctctaccatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCAAGGGGGATGCAGTGAAGCAGGAGGTTGATCGGAACGAGGACATGATCCG

Basic information

species Zea mays
transcript GRMZM2G168629_T04
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168629_T01 (Zea mays), 3'ss of exon 27
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 27
gtttgttctaacaaccaagaaccttgtaagtgacattgcaagcggttccgatgt--tgctctga--------------tgttgcagctctaccatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCAAGGGGGATGCAGTGAAGCAGGAGGTTGATCGGAACGAGGACATGATCCG
|||||||     || | ||  ||||    | ||  || ||  || | |  |||   | ||||||              | ||    || | |  | |||||  |||||||  ||||||| || || |||||||||||||  |||||||||||||| |||||||||||||| ||||||||||| || || |||||||| ||
gtttgttgccttaatctaggtccttacggg-gatgtttcatacgatgcaaatgccctactctgagttctttttgctaatattcttactatgctgtctcagTTTTGGACTCATTAGTTGACCCCATTGAGAAAACTATAAATCACAAACCCAAGGGCGATGCAGTGAAGCAAGAGGTTGATCGCAATGAAGACATGATTCG
















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|166696612|gb|EG174558.1|EG174558
EST:     TTTGATTCTATCAAAGCTAGCAGACAATTGCCCTTCCGCCGTCCTTGCTG                         TCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAG
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAG
EST: gi|32924248|gb|CF029060.1|CF029060
EST:     TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG                         TCCTGGACTCCATAGTTGAACCAATCGAGAAAATTATAAGCCACAAACCCA
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
EST: gi|32924416|gb|CF029228.1|CF029228
EST:     TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGGCCTTGCTG                         TCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
EST: gi|32923836|gb|CF028648.1|CF028648
EST:     TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG                         TCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
EST: gi|166410228|gb|EG043938.1|EG043938
EST:     TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG                         TCCTGGACTCCATAGTTGAACCAATCGAG
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGAACCAATCGAG
EST: gi|40335220|gb|CK369290.1|CK369290
EST:     TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCATCCGCCGTCCTTGCTG                         TCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
EST: gi|32923972|gb|CF028784.1|CF028784
EST:     TTTGATTCTATCAAAGCTGGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG                         TCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
EST: gi|29544507|gb|CB604887.1|CB604887
EST:     TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG                         TCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
EST: gi|50322915|gb|CO518041.1|CO518041
EST:     TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG                         TCCTGGACTCCATAGTTGA
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGA
EST: gi|33095774|gb|CF055768.1|CF055768
EST:     TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG                         TCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
EST: gi|32923875|gb|CF028687.1|CF028687
EST:     TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG                         TCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA
genomic: TTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTGgtttgttcta ... accatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgacattgcaagcggttccgatgttgctctgatgttgcagctctaccatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCAAGGGGGATGCAGTGAAGCAGGAGGTTGATCGGAACGAGGACATGATCCG
                           ctctgat  putative branch site (score: 4)
                                         ctctacc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttctaacaaccaagaaccttgtaagtgacattgcaagcggttccgatgttgctctgatgttgcagctctaccatttcagTCCTGGACTCCATAGTTGAACCAATCGAGAAAACTATAAGCCACAAACCCAAGGGGGATGCAGTGAAGCAGGAGGTTGATCGGAACGAGGACATGATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC