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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttcaaacctgtactttgtactgctttctctcttaattgattggcagagctcctgccttttcgttaaaaaaaatacatgacaatttattgtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGAGCCAGAAGGACA

Basic information

species Zea mays
transcript GRMZM5G879882_T03
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 13
-------------------------------tgttcaaacctgtactttgtactgctttctctcttaattgattggcagagctcctgccttttcgttaaaaaaaatacatgaca---attt----attgtgacaa-cagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGAGCCAGAAGGACA
                               | | |    |     ||   ||   || | |||   |   |||  ||    |      ||  | || || |     |||||||   ||||     || |||||| |||||||||||||| ||||| |||||||| | |||||| |||||||||||||| |||||| |||| || |||||||| || || |||||||||||||||||||
gtgagtacaaatttttgtattaccttaattttctccggttcccagattcaaacatattaccctc---aacaattatcatgaattaaatattaccctttaacagttcgcatgacatcaatttttgtgttctgacaaacagAGGGTAACATCAACAAGAAACAAGGTTAAGATAACCGACAGGATGTGGGCAAGGCTGTTGTCCTCGACCAACCAGCCCAGCTTCCTGAGCCAGAAGGACA

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 13
lower sequence: AT4G29220.1 (Arabidopsis thaliana), 3'ss of exon 12
tgttcaaacctgtactttgtactgctttctctcttaattgattggcagagctcctgccttttcgttaaaaaaaatacatgacaatttattgtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGAGCCAGAAGGACA
 ||      | | ||    ||||     |   | | |     |   | |  |    |  ||| |  |    ||  |||||    || | | |      ||||| | ||    | |  ||||||||||  ||| |||||||| ||||||||||||||  ||||||| || ||||||||||||||| |||  ||    ||||
-gtgagtctcaggaccaaatact-----catacctgagcatctcttacatttatatcaatttgggaatcctaataacatggt--ttgaatattgtg-tagAGGATCACGGAGAAACAGAACAAGGTGGTGATCACTGACAGAATGTGGGCGAGGCTTTTGTCTTCGACGAACCAACCGAGTTTCATGAAGCAAGCTGACA
















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|32858441|gb|CD998122.1|CD998122
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|91876347|gb|EB406304.1|EB406304
EST:     GCTTTCCAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTCCAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGGG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|74238195|gb|DT646109.1|DT646109
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|37401035|gb|CF637880.1|CF637880
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|37382133|gb|CF627993.1|CF627993
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|4967240|gb|AI691913.1|AI691913
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGA
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGA
EST: gi|40336088|gb|CK370158.1|CK370158
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|16926962|gb|BM080030.1|BM080030
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|76286570|gb|DV026138.1|DV026138
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTCCAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|113703664|gb|EE681168.1|EE681168
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|4966450|gb|AI691306.1|AI691306
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|4609847|gb|AI600686.1|AI600686
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|91876348|gb|EB406305.1|EB406305
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|5688732|gb|AI941747.1|AI941747
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|120480265|gb|EH210787.1|EH210787
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATTTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGGG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|108954346|gb|EC365109.1|EC365109
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|211050013|gb|FL347978.1|FL347978
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|120480087|gb|EH210728.1|EH210728
EST:     GGCATGCATATATACCATTTCAT                         AGGGTAACATTTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|148999634|gb|EE036619.2|EE036619
EST:     CCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: -CTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|86474334|gb|DY240704.1|DY240704
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
EST: gi|6540652|gb|AW225314.1|AW225314
EST:     GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCAT                         AGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG
genomic: GCTTTACAGTCGGAATGGTTAATGGCAGGCATGCATATATACCATTTCATgtgagtacaa ... gtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagagctcctgccttttcgttaaaaaaaatacatgacaatttattgtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGAGCCAGAAGGACA
                   ttaaaaaaaatacatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttcaaacctgtactttgtactgctttctctcttaattgattggcagagctcctgccttttcgttaaaaaaaatacatgacaatttattgtgacaacagAGGGTAACATCTACAAGGAACAAGGTGAGGATAACTGACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGAGCCAGAAGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - -acctgta
- - - - - - - - - gtactgc
- - - - - - - - - - - - - - - - - - -ttgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacatg