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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAAAGATGGGTATGTGAGCAAGGATGAGATGATCCAAGCAATAAACGAGACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttctatttcttggtagctctatacctactagtcttttgtgtaaagtaaaccaccacatttttggttggacaactctcttcctacctactagtc...

Basic information

species Zea mays
transcript GRMZM2G006790_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006790_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 5'ss of exon 4
AATAAAGATGGGTATGTGAGCAAGGATGAGATGATCCAAGCAATAAACGAGACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttctatttcttggtagctctatacctactagtcttttgtgtaaagtaaaccaccacat--ttttggttggacaactctcttcctacctactagtc-
|| |||||||| ||||| || ||||| |||||| | ||| |||| || |||||  | ||||| || ||||||||||||| |||||||||||||||||||||| |||    | ||       |||||| |     ||    ||  |   |||  ||        ||    || | || |||  |        |  ||    |  
AACAAAGATGGATATGTCAGTAAGGAAGAGATGGTTCAATCAATGAATGAGACTGCAACAGGGGAACGCTCTTCTGGGCGTATAGCCATGAAAAGATTTGgtaagtcgcttgttctcc---agctctctggtctctgagtttagggcgaaaacaattagttgtatgcccttagatgtacatgttatgaataaattatattttt

upper sequence: GRMZM2G006790_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G16060.1 (Glycine max), 5'ss of exon 5
AATAAAGATGGGTATGTGAGCAAGGATGAGATGATCCAAGCAATAAACGAGACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttctatttcttggtagctctatacctactagtcttttgtgtaaagtaaaccaccacatttttggttggaca-actctcttcctacctactagtc
|| || ||||| ||||| |||||  |||||||| ||||||| ||||| || || ||  |||| ||||| ||||||||    |||||||||||||||||||||||||| ||| || |||      | || |  | |   |           || |  | | |    ||       |||| ||||  ||   |     |  | 
AACAAGGATGGATATGTCAGCAAAAATGAGATGGTCCAAGCTATAAATGAAACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttgtctcttcctttccc-ttttaaatatgcatataagccccaatgaggattcaagcttgcttaaacacagacatactcagttatcagggtgtgtta

upper sequence: GRMZM2G006790_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G33830.1 (Glycine max), 5'ss of exon 5
AATAAAGATGGGTATGTGAGCAAGGATGAGATGATCCAAGCAATAAACGAGACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttctatttcttggtagctctatacctactagtcttttgtgtaaagt-aaaccacca--catttttggttggacaactctcttcctac-ctactagtc
|| || ||||| ||||| |||||  |||||||| ||||||| |||||||| || ||  |||| ||||| ||||||||    |||||||||||||||||||||||||| ||| |  |||  |  || | |   ||     | |   | |||  | |||  | ||  ||   ||| ||  |||      | |  |   ||  ||  
AACAAGGATGGATATGTCAGCAAAAATGAGATGGTCCAAGCTATAAACGAAACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatctctccctt--tccctttgtgtgtaaataacatgcatataagctcaaatgagcattcaagcttgcttaaacacaggcatactcatgttatcag--

upper sequence: GRMZM2G006790_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv19s0015g01200.t01 (Vitis vinifera), 5'ss of exon 4
AATAAAGATGGGTATGTGAGCAAGGATGAGATGATCCAAGCAATAAACGAGACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttctatttcttggtagctctat-acctactagtcttttgtgtaaa-gtaaaccaccacatttttggttggaca-actctcttcctacctactagtc
||||| ||||| ||||||||||||   |||||| | || |||||||| || || ||  |||| ||||| ||||||||    ||||||||||||||||| |||||||  ||    |||   |  || | | |   | | |  ||      |       |       |||| |   | |||  |   ||||  |   ||||    
AATAAGGATGGTTATGTGAGCAAGAGCGAGATGGTGCATGCAATAAATGAAACAACTGCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTCGgtcagtcctcctcctctctatcactttctcatacagtggctttgcacacactcacggatatgtgaatttatatatagacccagattctttttcaatactg---

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|113675155|gb|DW829924.1|DW829924
EST:     ACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCAATGAAAAGATTTG                         AGGAAATGGACTGGGAC
genomic: ACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCA-TGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGAC
EST: gi|50324727|gb|CO519853.1|CO519853
EST:     GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTG                         AGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT
genomic: GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAAAGATGGGTATGTGAGCAAGGATGAGATGATCCAAGCAATAAACGAGACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttctatttcttggtagctctatacctactagtcttttgtgtaaagtaaaccaccacatttttggttggacaactctcttcctacctactagtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA