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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattatgtgttcatagatgtttcagatatttgatagattccatgcgact...

Basic information

species Zea mays
transcript GRMZM2G006130_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 7
GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattatgtgt-tcatagatgtttcagatatttgatagattccatgcgact----
||||||||||| ||||||||||||||||| ||| | ||||| || |||||||||||||||||||| |||||||||  || | ||||| |||| |||||||||||||| || | |  | ||||   |    | ||   |||  || |  |  || | |   | ||  | | |    
GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagctatattttcccattgaaaatcaagttcttgatatgtacatatatgccagacatgtctgggataattgacttgatttaca---ttcaaacaattgtag

upper sequence: GRMZM2G006130_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 7
GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattatgtgttcatagatgtttcagatatttga--tagattccatgcgact--------
||||||||||| ||||||||||| ||||| ||| | ||||| || |||||||||||||||||||| |||||||||  || | |||||  ||| |||||||||||||| || | || ||||||||       ||| |  ||| |  |||| ||||  |   |||||| | |          
GGACATGGTTTTCGCACAGAACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagctatattttccaattgaaaatcaagttcttgatatctgcacatatatg------tcagacgtgtctgggataattgacttgatttccattcaaacaattgtag
















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|211353136|gb|FL044613.1|FL044613
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|18661865|gb|BM501621.1|BM501621
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350733|gb|FL044606.1|FL044606
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|32924555|gb|CF029367.1|CF029367
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350735|gb|FL044608.1|FL044608
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTANAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350722|gb|FL044595.1|FL044595
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGANATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211150003|gb|FL374637.1|FL374637
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350723|gb|FL044596.1|FL044596
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350730|gb|FL044603.1|FL044603
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|18654845|gb|BM499650.1|BM499650
EST:     ACTTATATCCATGCTTNTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211353135|gb|FL044612.1|FL044612
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350729|gb|FL044602.1|FL044602
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350731|gb|FL044604.1|FL044604
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211079656|gb|FL402147.1|FL402147
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAAAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350725|gb|FL044598.1|FL044598
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211221447|gb|FL389601.1|FL389601
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|32924412|gb|CF029224.1|CF029224
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|8367922|gb|BE050867.1|BE050867
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350734|gb|FL044607.1|FL044607
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350727|gb|FL044600.1|FL044600
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|18963147|gb|BM660266.1|BM660266
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350728|gb|FL044601.1|FL044601
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGNTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|32924548|gb|CF029360.1|CF029360
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211353132|gb|FL044609.1|FL044609
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350732|gb|FL044605.1|FL044605
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
EST: gi|211350724|gb|FL044597.1|FL044597
EST:     ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG                         GAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG
genomic: ACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactg ... actactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattatgtgttcatagatgtttcagatatttgatagattccatgcgact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatcaa