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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttacttgattcaaatgcttccttttttgtgaacactccttaggataattggttttattgcaagtatgtatatgcatacctacagtattagggtt...

Basic information

species Zea mays
transcript GRMZM2G057329_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g59700.1 (Oryza sativa), 5'ss of exon 6
TTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttacttgattcaaatgcttccttttttgtgaacactccttaggataattggttttattgcaagtatgtatatgcatacctacagtattagggtt--
||||||||||| |||||||| ||||| ||||| |||||||| |||||||| ||||||||||| |  ||   ||  |||||||  |  | |  || ||    |         ||   || |    ||||||| | |   ||| |||||  | |   |   
TTCTTTATAACTTGTGCAAAATGTGAATGGCTGGACAACAAGCATGTGGTTTTTGGGgtaagttccctcattttgaatgctttgtgctctcggagcaacattccaacagcatgtacttgtctacagtatgtttttt--tacttacagagtaaatatatg

upper sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G37190.1 (Glycine max), 5'ss of exon 6
TTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagctt-acttgattcaaa-tgcttccttttttgtgaacactccttaggataat-tggttttattgcaagtatgtatatgcatacctacagtattagggtt
|||||||||||||||||||| || |||||||||||||| || ||||| || ||||||||| |||| |||   |||  | |||       | | | ||   | |||   | |   ||  | |      ||| |||   |  ||   |     |  ||    
TTCTTTATAACATGTGCAAAATGCGACTGGCTTGACAAAAAGCATGTTGTCTTTGGGgtatgcttcactatcttcggagtgcggttgcatatattaattattcttcaaacagcctgaatgtgaatttagt-tgttcctcaatgtttgttacac-agtac-

upper sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G11960.1 (Glycine max), 5'ss of exon 6
TTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagctt-acttgattcaaatgcttccttt------tttgtgaacactccttaggataatt-ggttttattgcaagtatgtatatgcatacctacagtattagggtt
|||||||||||||||||||| |||||||||||||||||||| ||||| || ||||||||| |||| |||   ||||  ||| |   ||      | |   ||||  |   | |  ||||  |||||  | |||| |||  | ||  |||  | ||||  |     
TTCTTTATAACATGTGCAAAATGTGACTGGCTTGACAACAAGCATGTTGTCTTTGGGgtatgcttcactatcttcagttgcatatattaaatattctccaaacagcctgaatgtgaatttagtttttcttcaaggatgcgtttgt-tac--atagtacaa-----

upper sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G26260.1 (Glycine max), 5'ss of exon 6
TTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagctt-acttgattcaaatgcttccttt------tttgtgaacactccttaggataatt-ggttttattgcaagtatgtatatgcatacctacagtattagggtt
|||||||||||||||||||| |||||||||||||||||||| ||||| || ||||||||| |||| |||   ||||  ||| |   ||      | |   ||||  |   | |  ||||  |||||  | |||| |||  | ||  |||  ||||||  |     
TTCTTTATAACATGTGCAAAATGTGACTGGCTTGACAACAAGCATGTTGTCTTTGGGgtatgcttcactatcttcagttgcatatattaaatattcttcaaacagcctgaatgcgaatttagtttttcttcaaggatgggtttgt-tac--acagtacaa-----

upper sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0084g00620.t01 (Vitis vinifera), 5'ss of exon 5
TTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttacttgattcaaatgcttccttttttgtgaacactccttaggataattggttttattgcaagtatgtatatgcatacctacagtattagggtt-
|||||||| |||||  | || |||||||||||||||||||| ||||||||||| |||||| | |  ||    ||     ||     || | || | | || ||        ||     |     | ||||| | |  | |    || | |  |   | 
TTCTTTATCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctctaatctcttgccctctgggttctttgtaaagtctttcaatatgctgaaaccaaaaatattatgtct-tttacaagaccaatgtctgttctt

upper sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ31848 (Selaginella moellendorffii), 5'ss of exon 6
TTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttacttgattcaaatgcttccttttttgtgaacactccttaggataattggttttattgcaagtatgtatatgcatacctacagtattagggtt
||||||||||| || || || || |||||||| |||||||| |||||||| ||||| ||||| |    | |  |    ||| |     |  ||  |  |  ||   |                                                  
TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttcttctcaaacttgagctgcaaaactcatgctctattttttccag-------------------------------------------------

upper sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ38013 (Selaginella moellendorffii), 5'ss of exon 6
TTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttacttgattcaaatgcttccttttttgtgaacactccttaggataattggttttattgcaagtatgtatatgcatacctacagtattagggtt
||||||||||| || || || || |||||||| |||||||| |||||||| ||||| ||||| |    | |  |    ||| |     |  ||  |  |  ||   |                                                  
TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttcttctcaaacttgagctacaaaactcatgctctattttttccag-------------------------------------------------

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|113808548|gb|DW929323.1|DW929323
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGG
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGG
EST: gi|166563094|gb|EG191235.1|EG191235
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGC
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGC
EST: gi|211023124|gb|FL428614.1|FL428614
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAARATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|19058424|gb|BM737091.1|BM737091
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|32858929|gb|CD998610.1|CD998610
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|60349165|gb|DN216138.1|DN216138
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|60349812|gb|DN216785.1|DN216785
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|60394638|gb|DN227508.1|DN227508
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|24766439|gb|CA401593.1|CA401593
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAAACGGTTTGCTCGTCGTGAGGAAAATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|87152302|gb|DY397091.1|DY397091
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGA
EST: gi|32925862|gb|CF030674.1|CF030674
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|211438423|gb|FL465204.1|FL465204
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|211073855|gb|FL392646.1|FL392646
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|211027097|gb|FL381991.1|FL381991
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGTAAATGTT
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTT
EST: gi|211206179|gb|FL469079.1|FL469079
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|32933536|gb|CF038348.1|CF038348
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|6695399|gb|AW288507.1|AW288507
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCT
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCT
EST: gi|32926451|gb|CF031263.1|CF031263
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|32940102|gb|CF044921.1|CF044921
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAAATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|8577336|gb|BE129973.1|BE129973
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|211433999|gb|FL392548.1|FL392548
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGT
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGT
EST: gi|12047274|gb|BF729413.1|BF729413
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|32827571|gb|CD967249.1|CD967249
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|78179385|gb|DV549758.1|DV549758
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|60398036|gb|DN230852.1|DN230852
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTGCTCGTCGTGAGGAAGATTGAAAATGTTGCA
EST: gi|166594681|gb|EG162196.1|EG162196
EST:     TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG                         AGAGTGCTTGGAGACGGTTTG
genomic: TAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttac ... tccaattcagAGAGTGCTTGGAGACGGTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttacttgattcaaatgcttccttttttgtgaacactccttaggataattggttttattgcaagtatgtatatgcatacctacagtattagggtt

- - - - - - -  GCAAAG