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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactttcttgggactaaaggctttgttgttttttcaagaaaaaaaaggctttgtcagtcgttgttattgcctcatatttactgaatttaaatttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTATCCTTCTCTTGGTGGAATGGAGTAT

Basic information

species Zea mays
transcript GRMZM5G825226_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825226_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g56230.5 (Oryza sativa), 3'ss of exon 4
aactttcttgggactaaaggctttgttgttttttcaagaaaaaaaaggctttgt---------cagtcgttgttattgcctcatatttactgaatttaaatttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTATCCTTCTCTTGGTGGAATGGAGTAT
         |  ||  | | |  |||| | |   ||   || || ||| | ||          || |   |  | ||||| ||| ||  ||||||| |||| |||  |||||||| | ||||| |||||| |||||||||||||| |||  |||||||||||||| ||||| ||||||||||||
---------gtaacatatgtcactgtt-tatccgcattgaataataggttatgctgatatatacattttctccttttgccacatgttagctgaatt-aaatctgtttagGTTTCTCTGGGGTACTTCATCGCTGACCTTGCTATGTTATCCTGGGCTTATCCTTCCCTTGGCGGAATGGAGTAT

upper sequence: GRMZM5G825226_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G03520.1 (Glycine max), 3'ss of exon 3
aactttcttgggactaaaggctttgttgtttt----ttcaagaaaaaaaaggctttgtc-agtcgttgttattgcctcatatttactgaatttaaatttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTATCCTTCTCTTGGTGGAATGGAGTAT
   | ||||  |  || ||    |  | || |    | ||| | |     |  ||| ||  ||| |     |||  | ||||||  |   ||| ||| || | |||| ||||| || || |||||| |||||||||  |||||||| |||  || ||||||||||||||||   ||||||
--atatcttacgtttatagatcatcatattatgagctgcaacacatttttgtttttatctggtcatgaaatttgtattatattt--tagtttttaatgtgac-agGTGTCTGTCGGTTACTTCATCGCTGACCTTGGGATGATATTTTGGTTTTTTCCTTCTCTTGGTGGATATGAGTAT

upper sequence: GRMZM5G825226_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G45240.3 (Glycine max), 3'ss of exon 4
--aactttcttgggactaaaggctttgttgtttttt-caagaaaaaaaaggctttgtc-agtcgttgttattgcctcatatttactgaatttaaatttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTATCCTTCTCTTGGTGGAATGGAGTAT
  |  | ||||  |  || ||    | || |    | ||| | |     |  ||| ||  ||| |     |||  | || ||   | ||||| ||| || | |||| ||||| || || |||||| |||||||||  |||||||| |||  || ||||||||||||||||   ||||||
atatatatcttatgtttatagatcatattatgagctgcaacacatttttgtttttatctggtcatgaaatttgtattatgtt---ttaatttcaatgtgac-agGTGTCTGTCGGTTACTTCATCGCTGACCTTGGGATGATATTTTGGTTTTTTCCTTCTCTTGGTGGATATGAGTAT

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|148934690|gb|EC878738.2|EC878738
EST:     ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGG                         GTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
genomic: ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGGgtaaaagctg ... atttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
EST: gi|71771875|gb|DR969812.1|DR969812
EST:     ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGG                         GTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
genomic: ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGGgtaaaagctg ... atttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
EST: gi|76925225|gb|DV170328.1|DV170328
EST:     ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGG                         GTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
genomic: ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGGgtaaaagctg ... atttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
EST: gi|21330525|gb|BQ485906.1|BQ485906
EST:     ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGG                         GTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGC
genomic: ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGGgtaaaagctg ... atttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGC
EST: gi|78082331|gb|DV510743.1|DV510743
EST:     ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGG                         GTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
genomic: ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGGgtaaaagctg ... atttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
EST: gi|78112273|gb|DV530667.1|DV530667
EST:     ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGG                         GTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
genomic: ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGGgtaaaagctg ... atttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
EST: gi|74237536|gb|DT645450.1|DT645450
EST:     ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGG                         GTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
genomic: ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGGgtaaaagctg ... atttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
EST: gi|149078049|gb|EE166790.2|EE166790
EST:     ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGG                         GTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
genomic: ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGGgtaaaagctg ... atttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
EST: gi|76918369|gb|DV167265.1|DV167265
EST:     ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGG                         GTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
genomic: ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGGgtaaaagctg ... atttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
EST: gi|87154553|gb|DY399342.1|DY399342
EST:     ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGG                         GTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT
genomic: ATGGACTAGTAACTTATCGGAGTTCAAATCTATCCAATTTCACTTTGGGGgtaaaagctg ... atttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggctttgtcagtcgttgttattgcctcatatttactgaatttaaatttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTATCCTTCTCTTGGTGGAATGGAGTAT
                                              tttgtcc  CT-rich tract
                          tcatatttactgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactttcttgggactaaaggctttgttgttttttcaagaaaaaaaaggctttgtcagtcgttgttattgcctcatatttactgaatttaaatttgtccagGTTTCTGTTGGGTATTTCATCACTGACCTTGCTATGATATTATGGGCTTATCCTTCTCTTGGTGGAATGGAGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA