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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgtgtctatcccgtccgacactggccatggggccatgctatttatggatatcaactcaactgaccactcttccattgtgaattacaatttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG

Basic information

species Zea mays
transcript GRMZM2G172322_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172322_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g06740.1 (Oryza sativa), 3'ss of exon 6
gattgtgtctatcccgtccgacactggccatggggcca-tgctattta----tggatatca--actcaactgaccactcttccattgtgaattaca-atttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG
        |  | | ||    |||||   ||  |   | |  |||||     ||| |||      || | ||    ||| |  |||||||||| || |  |||| ||||||| |||| ||||| || |||||||||||||| || |||||||||||||||||||| ||||||
--------catttcagtatttcactgtttatcagttaaattttatttggttttggttattgttgttccattggatgctccttgattgtgaattgcacaaatttgacagAGCTGTACCATCTGCCGTTTTCTCCCAACCACCCATCGGACAAGTTGGTCTTACTGAAGAGCAG

upper sequence: GRMZM2G172322_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G16010.1 (Glycine max), 3'ss of exon 6
gattgtgtctatcccgtccgacactggccatggggccatgctatttatggat-atcaactcaactgaccactcttccattgtgaattacaatttttggca----gAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG
     || | ||    |  ||   |   |||     | |      | ||  | |  || |||  |  || | |  |   | |   ||| | |  ||  ||    ||||| | ||||||||||| || || ||||||||||| ||||||||||||||||||||||| |||
--acatgcccatgaaattggatggtactcatcatagcttctctgctgtgttttagtaattca--tagcctcccaactgat-tctgttatattccttatcatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAG

upper sequence: GRMZM2G172322_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G03740.2 (Glycine max), 3'ss of exon 6
gattgtgtctatcccgtccgacactggccatggggccatgctatttatggatatcaactcaactgaccactcttccattg--tgaattacaatttttggca----gAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG
     || | ||    |  ||   |   ||| |   | |    | |   | | |      || | |   |    | | ||  |   ||| | |  |    |    ||||| | ||||||||||| || || ||||||||||| ||||||||||||||||||||||| |||
-----tgcccatgaaattggatggtactcatcgtagcttatactctgctg-tgttttagtaattcatagcctcccaactgattctgttatattcctcattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAG

upper sequence: GRMZM2G172322_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0141g00390.t01 (Vitis vinifera), 3'ss of exon 6
gattgtgtctatcccgtccgacactggccatggggccatgctatttatggata----tcaactcaactgaccactcttccattgtgaattacaatttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG
     ||   |    |||  | ||  |   || |   |     |  | || ||    | | ||  | |  | ||    | |   ||  ||    || |  |||||||| |||| ||||||||||| ||||| ||||| || |||||||||||||||||||| || |||
--ccctgagaaggaagtctaatacaagtt-tgagtttaaatggtaaaaggctaagtttgatctgtattagctacctgactagattgt-ttcttcttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG

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|149037276|gb|EE155319.2|EE155319
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|211393001|gb|FL405406.1|FL405406
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|60359695|gb|DN226668.1|DN226668
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|211356738|gb|FL440505.1|FL440505
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|148956137|gb|EC901907.2|EC901907
EST:     CATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: CATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|149101004|gb|EE187101.2|EE187101
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|71319218|gb|DR796369.1|DR796369
EST:     GCATTGGCGAAAACTGTCTTTGGCAATGAACCTACCAACCCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|93017205|gb|EB642725.1|EB642725
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAACCCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|211356737|gb|FL440504.1|FL440504
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTCCCCAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCCAACCACCAATAGGACAAGTTGGTC
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCT-CCCAACCACCAATAGGACAAGTTGGTC
EST: gi|211484881|gb|FL392986.1|FL392986
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|76932106|gb|DV172946.1|DV172946
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|60398346|gb|DN231162.1|DN231162
EST:     AAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: AAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggatatcaactcaactgaccactcttccattgtgaattacaatttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG
               aactgac  putative branch site (score: 2)
                                             ttttt  putative PPT
                                   tgaattacaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgtgtctatcccgtccgacactggccatggggccatgctatttatggatatcaactcaactgaccactcttccattgtgaattacaatttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG