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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgacatattcccttgtccaaatgaatattcgttcttgctcttgtataatttgacagatctgacgcggaaatattaaattttatctgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG

Basic information

species Zea mays
transcript GRMZM2G075153_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075153_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g25940.4 (Oryza sativa), 3'ss of exon 3
---------gttcgacatattcccttgtccaaatgaatattcgttcttgctcttgta---taatttgacagat--ctgacgcggaaatattaaattttatctgctc-cttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG
         | | | |    |  | |    |  ||     | |   || ||| |  |     |||||  ||||  |      | |||| |||||  ||  ||  || || |||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||
gttagaaatgattggcgatctttcgtaaatagttggggggttgcaattactcctacaaatcgatttggtagatgccctttttgcaaatgttaaaaatttcctcttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACTGAGGCATTGGAGAAGAAGATGAG
















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|211234235|gb|FL407898.1|FL407898
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|38229609|gb|CF919922.1|CF919922
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|30705385|gb|CD058765.1|CD058765
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|149074757|gb|EE163186.2|EE163186
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|30705650|gb|CD058859.1|CD058859
EST:     TACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: TACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|211223662|gb|FL398674.1|FL398674
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACC-GACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|148948278|gb|EC893795.2|EC893795
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|89758469|gb|DY687640.1|DY687640
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|29946125|gb|CB815991.1|CB815991
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|149108488|gb|EE189677.2|EE189677
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|211066604|gb|FL423906.1|FL423906
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
EST: gi|91873684|gb|EB403641.1|EB403641
EST:     ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG
genomic: ACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTTTAAGgttcgacata ... tgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtataatttgacagatctgacgcggaaatattaaattttatctgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG
                 atctgac  putative branch site (score: 3)
                                      ttttatctgctcctt  putative PPT
                            aaatattaaattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgacatattcccttgtccaaatgaatattcgttcttgctcttgtataatttgacagatctgacgcggaaatattaaattttatctgctccttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG