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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtag

Basic information

species Zea mays
transcript GRMZM5G829894_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G829894_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 5'ss of exon 5
CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtag
| ||||| |||||||||||||||||||| || ||| |||||||||||||||||||||||||||| |||||||| || ||||||||||||| |        ||||||  |      |||  | |||| ||   ||  ||  ||  || |   ||| ||||       | ||   |||  |||| ||
CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAAGAATTGAGGACGCTGGGGGCTTCGTGATGTGGGCTGgtaat----ttcatgattccttt----gaaattatctattttgctttg-tacttgtaatgatcattggttctttctaacggttgaacgac-tttgcag

upper sequence: GRMZM5G829894_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G33690.2 (Glycine max), 5'ss of exon 6
CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattcctctgattctatctataaaaagaaact-atcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtag
| ||||| |||||  | |||||||| || || || || |||||||| | ||| ||||| || ||||| || |||||||||||||||||||  |    ||   | |   | | |   |    | | ||    ||||  | | || |  ||  |    ||  |   ||   |||   |          
CCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGTTTTGTTATGTGGGCTGgtaaggtcatcttatagttagtttttgttatttgatttatagattcttgttgtttgtctctatggaaattttaaacactatgtttacag----------

upper sequence: GRMZM5G829894_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G06250.1 (Glycine max), 5'ss of exon 6
CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtag
| ||||| |||||  | ||||||||||| || || || |||||||| ||||| ||||| || ||||| ||||||||||||||||| |||| ||    |  | |   |||    |     |   |   |||| | | | |       || |  || || |     |||||      | || |  ||
CCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAGgtaatgtcatcattaaca-tatagtcagctttagttttatttatttaattctaaaaagata-taatgtttatctctgttgataacattacatatacag

upper sequence: GRMZM5G829894_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 5
CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattcctctgattct--atctataaaaagaaactatcttat---cttaatatgtgccattactgt----tgcttctactgcttgatttttcgaaatttgtag
| ||||| |||||  | |||||||| ||||| || || |||||||| ||||| ||||| || ||||| |||||||||||||||||||||| ||    | || ||  |  |  ||||   ||      | ||||   ||||||       ||   | |    ||||| |     |||||        || |  ||
CCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTGgtaatgtcatcactcatcattaacatatagtcagctttagttttatttacttaattcaaaaaatatatatataatgcttatcactattgataacatcgcatatacag

upper sequence: GRMZM5G829894_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G12220.1 (Glycine max), 5'ss of exon 5
CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgat-tcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgct-tctactgcttgatttttcgaaatttgtag
| ||||| |||||  |||||||||| || ||||| || |||||||| | ||| ||||| || ||||| ||||||||||||||||||||||  | | || |||  ||   | | |       |  |   ||||  ||| ||    | |   |||  || |  |     | |    |  |  |||  ||
CCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTGgtaaggttatcttctagttagctttttgtt----atttgatttattataagattcatcttgtttgtcactatggaaaatctaaacact--atgtttacag

upper sequence: GRMZM5G829894_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 5'ss of exon 6
CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtag
| ||||| || ||  | |||||||| |||||||| |  || ||| | |||||||||||||| ||||| || ||||| |||||||||||||   |  | | | | |             |||| | |||  ||||| | |||||   ||   ||   |  | ||    ||| | | |||       
CTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTGgtaagaaaacatttaact-------------gaaatt-tctcttctta-tttgtgcttatataatttgcttaattgg--aattatactaaaag-----

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|60398872|gb|DN231688.1|DN231688
EST:     AGATGAGAGACAAAGAATGGAGGACGCAGGGGGCTTTTTTATGTGGGTTG                         GGACATGGGGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGAAT
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTG-AT
EST: gi|166421171|gb|EG149350.1|EG149350
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGG
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGG
EST: gi|60359012|gb|DN225985.1|DN225985
EST:     ACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: ACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|31909593|gb|CD650996.1|CD650996
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|60341056|gb|DN208029.1|DN208029
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|60358897|gb|DN225870.1|DN225870
EST:     ATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: ATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|149099178|gb|EE185204.2|EE185204
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|71326203|gb|DR799792.1|DR799792
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|60399036|gb|DN231852.1|DN231852
EST:     ATGAGAGACAAAGGAATTGAGGACGCAGGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: ATGAGAGACAAA-GAATTGAGGACGCA-GGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|21481348|gb|BQ578031.1|BQ578031
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|33096324|gb|CF056318.1|CF056318
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtag

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