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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacacatgacctgcatcatagtgtcataacttgcagcagacagaaattcatagatgcttattttgcag

Basic information

species Zea mays
transcript GRMZM2G172322_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172322_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g06740.1 (Oryza sativa), 5'ss of exon 7
AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacacatgacctgcatcatagtgtcataacttgcagcagacagaaattcatagatgcttattttgcag
|||| |||| ||||| || |||||||||||||| || |||||||||||||||||||| |||||||| ||  || | |||  |||||    |    | |    ||  ||| ||  | | | |  ||  | || |||||
AGCTGTACCATCTGCCGTTTTCTCCCAACCACCCATCGGACAAGTTGGTCTTACTGAAGAGCAGgt-atagcatacgacgcgcatctatataaagtgatgcacaaaagaaagtcaattaaatttgtattttgtgcag

upper sequence: GRMZM2G172322_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G16010.1 (Glycine max), 5'ss of exon 7
AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtga-----tgacacatgacctgcatc--atagtgtca--taacttgcagcagaca-----gaaattcatagatgcttattttgcag---------------------
|||| | ||||||||||| || || ||||||||||| ||||||||||||||||||||||| |||||||     | |  ||    | |  ||  ||  | |||  |    | | | | |       ||| |  | ||||   | ||||||                       
AGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAGgtgagagaattatgcagtgtccggctctaatgctttcaaatggtcttctgaatattttaatgaattgtacagattaatgttttgctaacattttggtgatttgcacag

upper sequence: GRMZM2G172322_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G03740.1 (Glycine max), 5'ss of exon 7
AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac-atga---cctgcatc--atagtgtcataacttgcagcagaca-------gaaattcatagatgcttattttgcag---------------------
|||| | ||||||||||| || || ||||||||||| ||||||||||||||||||||||| |||||||    |  ||||    |||  ||  ||  | ||| |   |    || | |       ||| |    ||||   | ||||||                       
AGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAGgtgagagaattatgagtgtctgattctaatgctttcaaatggtcttccaaatattttaatgaattgtgcagattaatgttttgctaacattttggtgatttgcacag

upper sequence: GRMZM2G172322_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv07s0141g00390.t01 (Vitis vinifera), 5'ss of exon 7
AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacacatgacctgcatcatagtgtca--taacttgcagcagacagaaattcatagatgctta--ttttgcag
|||| |||| ||||||||||| ||||| ||||| || |||||||||||||||||||| || ||||||||| ||  |  | |   |  | |   ||  | |  | || |     |  ||| |||  ||  |   ||||| ||
AGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAGgtgatgccaattctcttctgtatttgcagcagctgagattcatccctt-gcgattaatatttgaatcatttttgtag

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:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|211393001|gb|FL405406.1|FL405406
EST:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|60359695|gb|DN226668.1|DN226668
EST:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|211356738|gb|FL440505.1|FL440505
EST:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|148956137|gb|EC901907.2|EC901907
EST:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTTCTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTTTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|149101004|gb|EE187101.2|EE187101
EST:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|71319218|gb|DR796369.1|DR796369
EST:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|93017205|gb|EB642725.1|EB642725
EST:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|211356737|gb|FL440504.1|FL440504
EST:     TGTGTTCTCCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: TGTGTTCT-CCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|211484881|gb|FL392986.1|FL392986
EST:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|76932106|gb|DV172946.1|DV172946
EST:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
EST: gi|60398346|gb|DN231162.1|DN231162
EST:     CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG                         GCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC
genomic: CTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacac ... tattttgcagGCAATTGAAGAGTATGGAGATGTTGATGTCTTCGTTGCCAACTTCAGGCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAGgtgatgacacatgacctgcatcatagtgtcataacttgcagcagacagaaattcatagatgcttattttgcag

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