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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaaatcccagcaaaagaagttgtcgatcacattatttttgagattaactttttcttgttatgcatttattgatttatacccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGACCCAACTGAAGTGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAAC

Basic information

species Zea mays
transcript GRMZM2G044584_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 3
gttagtaaatcccagcaaaagaagttgtcgatcacattatttttgagattaactttttcttgttatgcatttattgatttatacccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGACCCAACTGAAGTGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAAC
||| |||  |  |   |    |   ||| ||  ||      |||  | || | | |||    || ||  ||   || ||| |   ||||||||||| ||||||||||||||||||| || ||||||||||||||||| ||||||||||||||||  ||||||||||||||  ||||||||||||| ||||| 
gtttgtatgtttc--tagctaatactgttgaatac-----cttttggttttattatttacaattgtgtcttatgtgtttttt---caaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGACCCAACTGAAGCAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAAT

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g06474.1 (Oryza sativa), 3'ss of exon 3
gttagtaaatc-ccagcaaaaga------agttgtcgatcacattatttt-tgagattaactttttcttgttatgcatttattgatttatacccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGACCCAACTGAAGTGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAAC
||  |||  |  | ||||||         |  ||| ||  || | ||||  |   | ||||  || | | |  ||      ||  ||| | ||   | |||||| ||||||||||||||||||| || ||||||||||||||||| || |||||||| || |||||||||||||||||| ||||||||||||||||||| 
gtctgtatgtttctagcaaatagtacttgaaatgttgaatacctcatttggttttactaacaattgcctatcctg------ttcgtttttccctcgaaagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAGGACCCAACCGAGGTGATTCGCAAAGCTGTGATGCGCATGCTTCCCCGCAAT

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G36450.1 (Glycine max), 3'ss of exon 4
-gttagtaaatcccagcaaaagaagttgtcgatcacattatttttgagattaactttttcttgttatgcatt---tattgatttatacc----caaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGACCCAACTGAAGTGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAAC
  ||    |||     ||       ||||  ||    ||   | ||   || | ||||   | |||| || |   | ||||  ||   |     |  ||||||| |||||||  | ||| ||||||  || ||||| || ||||  |||||||| |||||||| |||||||||||||| ||||| ||||| ||  | |||
ttttcaacaatattttcattgccgcttgtttatttggtttcatatgctctttaattttcagtattatccagtctattttgacataagtcatggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGACCCTACTGAAGTCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAAC

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G22420.1 (Glycine max), 3'ss of exon 4
gttagtaaatcc-cagcaaaagaagttgtcgatcacattatttttgagattaactttttcttgttatgcatt---tattgat-ttatacc----caaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGACCCAACTGAAGTGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAAC
  |   || |        |  |  ||| |  ||    ||   | ||   || | ||||   | |||| || |   | ||||  |||   |     |  ||||||| |||||||  | ||| ||||||  || ||||| || ||||  |||||||| |||||||| |||||||||||||| ||||| ||||| ||  | |||
-cttccaattgtattttcattgccgttttttatttggtttcatatgctctttaattttcagtattatccagtctattttgacattaggtcactgtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGACCCTACTGAAGTCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAAC

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|16378867|gb|BI992643.1|BI992643
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGGgttagtaaat ... acccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|33102772|gb|CF062732.1|CF062732
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGGgttagtaaat ... acccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|18385121|gb|BM418320.1|BM418320
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGGgttagtaaat ... acccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|13381725|gb|BG458280.1|BG458280
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGGgttagtaaat ... acccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|211282462|gb|FL053249.1|FL053249
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGGgttagtaaat ... acccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|87153153|gb|DY397942.1|DY397942
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGGgttagtaaat ... acccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|33095052|gb|CF055046.1|CF055046
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGGgttagtaaat ... acccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttgagattaactttttcttgttatgcatttattgatttatacccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGACCCAACTGAAGTGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAAC
                         ttatgcatttattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaaatcccagcaaaagaagttgtcgatcacattatttttgagattaactttttcttgttatgcatttattgatttatacccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGACCCAACTGAAGTGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC