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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgcaatgtgtttattatctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATAAGCAACCTTCAGCAATCTTCACAGCAGGCTGAGGATGCTCTTTCACAAG

Basic information

species Zea mays
transcript GRMZM2G030280_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030280_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g17260.1 (Oryza sativa), 3'ss of exon 8
gtatatgcaatgtgtttattatctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATAAGCAACCTTCAGCAATCTTCACAGCAGGCTGAGGATGCTCTTTCACAAG
                     | |||||    | | ||||| ||||    | |  ||      | |||   ||| |||  || |  |  | |  | |||| | |   | ||| || | |  | |   |||||||||||||||||||||| |||||||||||||| || ||||||||||||||||||  |||||||||||| |||||||| || ||||| ||||||||||||||||
---------------------tttcttg----ccattggag-agcatgttagtactt-----catatggcctttctttatttgcttatgaat--ttatttgagtaa-gagttactaaaagta-agaaaactgcagCTTCTTTCGACACAGCTTGAACCTCTCACTGAGCAGCAGCTGTCAGGGATAGCCAACCTTCAGCAGTCTTCACAACAAGCTGAAGATGCTCTTTCACAAG
















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|89106563|gb|DY576780.1|DY576780
EST:     GCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAG                         CTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
genomic: GCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
EST: gi|71426015|gb|DR807065.1|DR807065
EST:     AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAG                         CTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
genomic: AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
EST: gi|74232819|gb|DT640733.1|DT640733
EST:     AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAG                         CTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
genomic: AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
EST: gi|71426016|gb|DR807066.1|DR807066
EST:     GAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAAG                         CT-CTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTC
genomic: GAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAA-Ggtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTC
EST: gi|19437057|gb|BM953467.1|BM953467
EST:     AGAGGTGTTTTTAGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAG                         CTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
genomic: AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
EST: gi|211365702|gb|FL031151.1|FL031151
EST:     AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAG                         CTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
genomic: AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATAAGCAACCTTCAGCAATCTTCACAGCAGGCTGAGGATGCTCTTTCACAAG
                               tgctgat  putative branch site (score: 3)
                                  tgataaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgcaatgtgtttattatctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATAAGCAACCTTCAGCAATCTTCACAGCAGGCTGAGGATGCTCTTTCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG