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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacag

Basic information

species Zea mays
transcript GRMZM2G000645_T03
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaata--gcttggtacag
||||| || |||||||| |||||||||||||||||||||||||||||| | ||||| ||||| ||||||||||||||||||||||| || |||| |||||||| || || | ||| | ||| | | | |||| | |||| ||||||| || |||| | |||
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os06g05180.3 (Oryza sativa), 5'ss of exon 1
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatag--cttggtacag
|||||||||||||||||||| || |||| |||||||| || || | ||| | ||| | | | |||| | |||| ||||||| || |||| | |||
------------------------------------------------------------------GTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 16
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgt------tttctcgaaaacaatgcttcctttcctttgtagca--tctgttaatttctctgactaacaaatagcttggtacag
|| ||||| |||| ||||||||| |||||||||||||||||||||||| |||| ||||||||||| |||||| | |||||||| ||||| ||||| || | | | | | ||| ||| | | || |||| |||| || ||| | | || |||
GTAACTACGATGTTTCATTTGGACCGCCCTATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAAgtaagtgaaacttctgcttggattattcaaagttttaaattgcaataatcttgactatttttctgtttatcaa-ttgtttttctcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatct------gttaatttctctgactaacaaatagcttggtacag
|| |||||||||| ||||||||| || ||||||||||||||||||||| |||| | ||||||| || ||| | || ||||| || || ||||| || | ||||| || | || | |||| |||| | | | || | || |||
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagt-------ggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 5
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgt---tttctcgaaaacaatgcttcctttcctttgtagca-----tctgttaatttctctgactaacaaatagcttggtacag
|| |||||||||| ||||||||| || ||||||||||||||||||||| |||| | ||||||| || ||| | || ||||| || || ||||| || | | | || | | || | ||| ||| | ||| ||| | || | | |||
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAAgtaagtggatcaatggtttgcattattcaaaatctctcaatgcagtggtcctgattttttttcttcttttttaactgtgttactcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 16
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgt------tttctcgaaaacaatgcttcctttcctttgtagca--tctgttaatttctctgactaacaaatagcttggtacag
|| ||||| |||| ||||||||| ||||| |||||||||||||||||| |||| ||||||||||| |||||| | |||||||| ||||| ||||| || | | | | | ||| ||| || | || | || |||| || ||| | || | |||
GTAACTACGATGTTTCATTTGGACCGCCCCATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAAgtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaatcttgactacttttctgtttatcaattttttttct-cag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 20
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgta------tgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacag
|| ||||||||||||||| |||| || ||||||||||||||||| ||| | || || ||||| | |||||| | |||||||| ||||| ||||| |||||| | | | |||| | | |||||| | | | | |||| || | | || | ||||
GTAACTACAATGTATCATCTGGACCGTCCTATGTACTTGTTGGGTTATCTCGCTAATCAAAGCAGGGTTTATTTGATTGACAAAGAGTTCAAgtaagcagatgttttactgttatgattgctaacaatgttttgta--acttactgacttctgtgtccactttatgatt----acag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 16
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttc----ctttcctttgtagcatctgttaatttct--ctgactaacaaatagcttggtacag---
|| || ||||||||||||||||| ||||| ||||| ||||| || |||||||| |||||||| || ||||| | | ||||| || || ||||| ||| | | | | || || | | | | |||| | | || || | | | | | ||||| | |
GTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAAgtacgttcctttatatatgtttatttgagactgttttatcttgcatacataatttgctaacatatttccctttttcttgggaatgcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 16
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacag----
|| || ||||||||||||||||| ||||| ||||| |||||||||||| |||| | |||||||| |||| | | ||||| || || ||||| || | | || || || | | | ||| | ||||| || | || || |
GTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAAgtaagtgct-tagatttgtgtgtttatataattgagattgttctagaagtttctgatgctgttcccctgttttgtggatgcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 16
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctc------gaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacag----------
|| || ||||||| ||||||||| || |||||||| |||||||||||| | || || ||||| || || ||||| || ||||| ||||| |||| || || |||| | |||| | || || ||| ||| | | || || | | || | |
GTAACCACAATGTTTCATTTGGACCGGCCTATGTATTTGTTGGGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAAgtgagtggacttttggcagaaagggggagtggagggtggttgttgtat-tgctaacatcttt-attattaagttggtttttccttttcaatgcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 16
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagct-tggtacag-------
|| || || |||| ||| ||||| || |||||||| ||||| |||||| |||| | |||||||| ||||||||||| ||||| ||||| |||| | || | | | |||| | || | |||| | | ||| | | || | || ||
GTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAAgtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcag

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|18965038|gb|BM661357.1|BM661357
EST:     GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
genomic: GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
EST: gi|89106492|gb|DY576709.1|DY576709
EST:     GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
genomic: GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
EST: gi|22490520|gb|BU050443.1|BU050443
EST:     GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTT
genomic: GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG