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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttataaagctaagcgaaatcgctttggaagcaagttgatgaattctggatctgatgcattctgttcatgtgttgctgtgtag

Basic information

species Zea mays
transcript GRMZM2G159369_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159369_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 8
TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttataaagctaagcgaaatcgctttgg-aagcaagttgatgaattctggatctgatgcattctgttcatgtgttgctgtgtag
||||||||||||||| || || || ||||||||||| |||||||| ||||||||||| ||||| |||||||| ||| ||||||| || || | |  |||||| |    |  |  ||   |||    |||    |   || || |   | ||    ||  ||  | ||| ||  | || | ||||    
TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatata---gaaggtacttaaatacttaaatttacataatccaattccaatataatctattggt-tgcttctgtag--
















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|60400615|gb|DN233422.1|DN233422
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|60349176|gb|DN216149.1|DN216149
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|33101695|gb|CF061655.1|CF061655
EST:     CCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: CCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|148932685|gb|EC876639.2|EC876639
EST:     ATGAGAAG-GTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|86466435|gb|DY232805.1|DY232805
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|4647206|gb|AI622281.1|AI622281
EST:     TGTGGCACCAGCCGGGATCCAAAGGGCCNCCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: TGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|32857597|gb|CD997278.1|CD997278
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCGCCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|37380832|gb|CF627255.1|CF627255
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGTTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|60399092|gb|DN231906.1|DN231906
EST:     CGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTTTCAATGCT
genomic: CGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|24767522|gb|CA402664.1|CA402664
EST:     CGGGATCCAAAGGCCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: CGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|4646531|gb|AI491677.2|AI491677
EST:     CTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: CTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|37379835|gb|CF626683.1|CF626683
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|32940600|gb|CF045419.1|CF045419
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|78545093|gb|DV622591.1|DV622591
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|20513042|gb|BQ280228.1|BQ280228
EST:     ATAAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|31558598|gb|CD527810.1|CD527810
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|60350336|gb|DN217309.1|DN217309
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|113854582|gb|DW976283.1|DW976283
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGC
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGC
EST: gi|33091270|gb|CF051264.1|CF051264
EST:     AGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: AGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|60356885|gb|DN223858.1|DN223858
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|148961931|gb|EE012723.2|EE012723
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCTTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|37388199|gb|CF631306.1|CF631306
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|101386448|gb|EB815241.1|EB815241
EST:     CTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: CTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|71326463|gb|DR799911.1|DR799911
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|14244876|gb|BG842814.2|BG842814
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|32934912|gb|CF039724.1|CF039724
EST:     ATCAG-AGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|9254367|gb|BE344835.1|BE344835
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|149096331|gb|EE182050.2|EE182050
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|67024988|gb|CO453737.1|CO453737
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|14244939|gb|BG842877.2|BG842877
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|21828690|gb|BQ703374.1|BQ703374
EST:     TGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: TGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
EST: gi|60358667|gb|DN225640.1|DN225640
EST:     ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAG                         GCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT
genomic: ATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttata ... tgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttataaagctaagcgaaatcgctttggaagcaagttgatgaattctggatctgatgcattctgttcatgtgttgctgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT