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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agataagttttaatgaaatcgaccaatgctgatccaatctgtttatctgtcatgtcaatcttgactaacgtaatatggatgccttcgtaaacatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT

Basic information

species Zea mays
transcript GRMZM2G055020_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055020_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g32060.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------------------------------agataagttttaatgaaatcgacc-----aatgctgatccaatctgtttatc---tgtcatg--tcaatcttgact-aacgtaatatggatgccttcgtaaacatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT
                                                                                      | |  |||| |  | |  ||  |      ||     ||  ||     || |    || |||   |||||  ||  | || | | |   |||||||||  ||||||||  |||| ||||||||||||||||||||||| ||||||||| |||| || |||||||||||||||  ||||||||||||||| || |||||||||||||||||
gtatctctcatctcgacgcatgattaataggatgcttaggtccggctataggagctgtcaagaactcaagatagcactgtctgcccaaactagttcttttcagttccgcataaaaaacatacatttaagaacattgtgcaatgccatagttcaatactgtttcaatgcattcgtgatgccttca-aaacatctccagGCCCAGCTTGAGAAGATTGCTCCAACTTGGATGAATATTTCGTTGAAAATGAAAGAGGATGTGGAGACAGACAAAGCTTTTGGATGGGTCTTGGAAAT

upper sequence: GRMZM2G055020_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 4
agataagtt--ttaatgaaatcgaccaatgctgatccaatctgtttatctgtcatgtcaatcttgactaacgtaatatggatgccttcgtaaacatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT
 |          |||   ||   || ||| |   | | | | |   | ||  |     | |  ||  |  |     |||||   ||   |     |||| ||| |  | |||  |||||||| || || ||||||||| |||| || || |||||||||||||  ||||| || ||||| || ||||||||  | |||||
-gcctgcccaactaacctaactaactaattcccttactaacagac-acctaactaacaactaatgggtgtctactgatggacttctctatttttttcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
















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|5468725|gb|AI834516.1|AI834516
EST:     TATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: TATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|71761576|gb|DR959513.1|DR959513
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|5895926|gb|AW037172.1|AW037172
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|32840194|gb|CD979875.1|CD979875
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|74237664|gb|DT645578.1|DT645578
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|78082143|gb|DV510555.1|DV510555
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCTTTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|32840195|gb|CD979876.1|CD979876
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|76015780|gb|DT942950.1|DT942950
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|5686756|gb|AI939849.1|AI939849
EST:     CTATTTCAAATATCGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|211541009|gb|FL454732.1|FL454732
EST:     TATTTCAAATA-TGATGCCTATGGGCAACTCTCCGGTGATAATCAAGAGG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCA-TACAGAAT
genomic: TATTTCAAATATTGAT-CCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTA-AAAAT
EST: gi|76917228|gb|DV166719.1|DV166719
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|71763634|gb|DR961571.1|DR961571
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|60347170|gb|DN214143.1|DN214143
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|78023550|gb|DV491937.1|DV491937
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|211218550|gb|FL110185.1|FL110185
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGACAACATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|211218551|gb|FL110186.1|FL110186
EST:     TTATAATCAAGAAG                         GCTCAGCTTGRGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: TTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|71760330|gb|DR958267.1|DR958267
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|60351853|gb|DN218826.1|DN218826
EST:     CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
EST: gi|148981075|gb|EE027418.2|EE027418
EST:     CTATTTCAATTA-TGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAG                         GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG
genomic: CTATTTCAAATATTGATCCTATTGGCAACTCTCCGGTTATAATCAAGAAGgtatctaatt ... acatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtcatgtcaatcttgactaacgtaatatggatgccttcgtaaacatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT
                 gactaac  putative branch site (score: 1)
                                              catcttt  putative PPT
                         taatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agataagttttaatgaaatcgaccaatgctgatccaatctgtttatctgtcatgtcaatcttgactaacgtaatatggatgccttcgtaaacatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA