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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacatagtccaaatgacactcccaagtgaagctgtagttatatactggaatatgtgaaattgtgaatatttttttctgacttctgtgcaatgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA

Basic information

species Zea mays
transcript GRMZM2G069631_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 3
---atacatagtccaaatgacactcccaagtgaagctgtagttatatactggaatatgtgaaattgtgaatatttttttctgacttctgtgcaatgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA
   ||       ||||   | |  | |           | |||||  |||   ||    ||| || | ||| | ||||||||| || | || ||| ||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||| || ||||||||||| ||||||||||| |
aggattatcttaccaagccatatgcactgcatgttagattgttattaact---atcctggaatttctcaatttgtttttctgatttatatgtaatccatgtagTTCGACTACCTAAAAAGTTTGGAAATAGAGGAGAAGATTAACAAGATCAAGTGGTGCCAAACAGCCAACAACGCCCTCTTTCTCTTATCTACAAATGATA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
atacatagtccaaatgacactcccaagtgaa-gctgtagttatatactggaatatgtgaaattgtgaatatttttttctgacttctgtgcaatgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA
           || |  || || |  || || ||||     | || || |   |   |||||  | |       ||| |||||| ||     ||  |  |||||||||| || || ||| |||||||||||||||| |||||||| ||||| |||||||||||| | ||   |||  | || ||  | || |||||||| |
---------gtaattttcagtcactggttaatgctgcc-cgaaatgcttgtggagcagaaatcttaa-----catttatgacttgtgattgttgttt-cagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 3
atacatagtccaaatgacactcc-caagtgaagctgtagttatatactggaatatgtgaaattgtgaatatttttttctgacttctgtgcaatgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA
           ||    || |     ||| | | || |   | || ||   ||  || | |    || |   | ||| | |  | ||  || ||  |  |||||||||| || || ||||||||||| |||||||| || ||||| ||||  |||||||||| | | ||   ||| ||||| ||  | ||||||||||| |
---------gtaatcatcatttggtcagtaatgttgcaccaacatcct---atgggtcagaa---gagtcaatatttataatgtatgatcattgttt-cagTTTGACTATCTTAAGAGTTTGGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 3
atacatagtccaaatgacactcc-caagtgaagctgtagttatatactggaatatgtgaaattgtgaatatttttttctgacttctgtgcaatgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA
           ||    || |     ||| | | || |   | || ||          | |  || ||||||| |     |  | ||  || ||  |  |||||||||| || || |||||||| || |||||||| || ||||| ||||  |||||||||||| | ||   ||| || || ||  | ||||||||||| |
---------gtaatcatcatttggtcagtaatgttgcaccaacatcctatgggtcagaaga--gtcaatatttata---aatgtatgatcattgttt-cagTTTGACTATCTTAAGAGTTTGGAGATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAACAGCTAATGGTGCCCTGTTCCTTCTTTCTACAAATGATA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 3
atacatagtccaaatgacactcccaagtgaa-gctgtagttatatactggaatatgtgaaattgtgaatatttttttctgacttctgtgcaatgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA
           || |  || || |  || || ||||   | | || || |   | |   || ||| || |||    | |||| | ||     ||  |  |||||||||| || || |||||||||||||||||||| |||||||| ||||| |||||||||||| ||||   |||  | || ||  | || |||||||| |
---------gtaattttcagtcactggttaatgctgcc-tgaaatgcttgtgga-gcagaaatgttaacatt----tatgacatgtgattgttgttt-cagTTTGACTATCTTAAGAGTTTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

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|89250814|gb|DY622600.1|DY622600
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGA
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGA
EST: gi|91873992|gb|EB403949.1|EB403949
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
EST: gi|67012325|gb|CO441074.1|CO441074
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
EST: gi|60340196|gb|DN207169.1|DN207169
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
EST: gi|148939774|gb|EC884472.2|EC884472
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
EST: gi|148991720|gb|EE033282.2|EE033282
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
EST: gi|94472892|gb|EB701850.1|EB701850
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggaatatgtgaaattgtgaatatttttttctgacttctgtgcaatgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA
                             ttctgac  putative branch site (score: 2)
          tgaaattgtgaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacatagtccaaatgacactcccaagtgaagctgtagttatatactggaatatgtgaaattgtgaatatttttttctgacttctgtgcaatgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA

- - - - - - - - - - - ccaagtg
- - - - - - - - - - - - - - - -gctgtag