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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAGGAGGAACCAGCTGATCTACCAGGACAAGCCGCGGCTCAAGACTGCGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacacccgtcttacgtgagcagtctaaacccgtccgtcgtcggcgcaggagaactctggttctgaatgtttgggcgcag

Basic information

species Zea mays
transcript GRMZM2G080320_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080320_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g21310.1 (Oryza sativa), 5'ss of exon 3
ATCAGGAGGAACCAGCTGATCTACCAGGACAAGCCGCGGCTCAAGACTGCGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacacc-cgtctt-acgtgagcagtctaaacccgtccgtc-gtcggcgcaggagaactctggttctgaa--tgtttgggcgcag----------------------------------------------------------------------
||||||| |||| ||||||| ||||||||||||||| |||||||||| ||  | |||||||||||||||||||||||| |||| |||||||||||  ||||| |||| || |||||| |  | | |    || |  |  |  |  ||   | ||     |   |||  || |      ||| |                                                                           
ATCAGGAAGAACAAGCTGATATACCAGGACAAGCCGAGGCTCAAGACCGCACTTGAGATGCTCAGGACCAGCATGTACGTAGAGGACAGCTTGTCCAAGgtatgtacccctcgtcttcaaatcaactcaatatatgcaccaattagttctcacatctttaggatggcactaagatcacttgagtatgatcttggccatgtaagatgacagtaagattatttgaatttgatcctgacaatgtaatgttttttttggcag
















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|31664393|gb|CD573118.1|CD573118
EST:     TGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: TGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|211301294|gb|FL411039.1|FL411039
EST:     CGCTGGAGATGCTCAGGGCCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|74236075|gb|DT643989.1|DT643989
EST:     CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|71324666|gb|DR799030.1|DR799030
EST:     TGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: TGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|71311760|gb|DR792325.1|DR792325
EST:     CGTTGGAGATGCTCAGGACCAGCAAGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|78075077|gb|DV503511.1|DV503511
EST:     CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|76011867|gb|DT939037.1|DT939037
EST:     CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|88748005|gb|DY532146.1|DY532146
EST:     CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCTTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|71442134|gb|DR823184.1|DR823184
EST:     CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|76933104|gb|DV173321.1|DV173321
EST:     CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|149075326|gb|EE163833.2|EE163833
EST:     AGGACCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: AGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
EST: gi|148949769|gb|EC895252.2|EC895252
EST:     CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAG                         GTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC
genomic: CGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacac ... ttgggcgcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAGGAGGAACCAGCTGATCTACCAGGACAAGCCGCGGCTCAAGACTGCGTTGGAGATGCTCAGGACCAGCATGTACATAGAAGACAGCTTGTCACAGgtacgtacacccgtcttacgtgagcagtctaaacccgtccgtcgtcggcgcaggagaactctggttctgaatgtttgggcgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG