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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGATCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttctttctcgtaacacaactctgatgccgggtcagaatgttctataaagattcaccaacatccacatcacagataatcaggcttgtgcgtacta...

Basic information

species Zea mays
transcript GRMZM2G177912_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 4
GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGATCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgt--tcgtttctttctcgtaacacaactctgatgccgggtcagaatgttctataaagattcaccaacatccacat-cacagataatcaggcttgtgcgtacta
||| ||||||||||||||||| ||||| || |||||  ||||||||||||| |||||||||||||| || |||||| ||||||| || ||||||||||||||  |    | |||| | |   || ||  | ||  |  ||||  |    | |   | ||  |      |  | ||     ||   | | |||    |     |
GTTTGTGTGGGATGAGGGCAAATACCCAACGATGTCACCGCTCAAGGAGATTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacctttttcccttgcgaccaca-taatcactagtcaagac--ccaacctacatatagtgctgttaatatgtttcgaccctaatgctgtctctagtca
















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|211359331|gb|FL325567.1|FL325567
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
EST: gi|9953349|gb|BE639932.1|BE639932
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCAGCAGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
EST: gi|78120131|gb|DV538515.1|DV538515
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
EST: gi|211267792|gb|FL344631.1|FL344631
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
EST: gi|211217973|gb|FL307283.1|FL307283
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCAGC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGC
EST: gi|71303539|gb|DR787880.1|DR787880
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTCCGAGCAGCGGAATATAACCATGTAAGGAGCCAGCTTACT
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACT
EST: gi|148969238|gb|EE019992.2|EE019992
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
EST: gi|149104624|gb|EE290073.2|EE290073
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
EST: gi|67016433|gb|CO445182.1|CO445182
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
EST: gi|211460898|gb|FL364621.1|FL364621
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
EST: gi|211078718|gb|FL360383.1|FL360383
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGC
EST: gi|76288290|gb|DV027858.1|DV027858
EST:     TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG                         GTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC
genomic: TCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttct ... tattttctagGTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGATCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgttcgtttctttctcgtaacacaactctgatgccgggtcagaatgttctataaagattcaccaacatccacatcacagataatcaggcttgtgcgtacta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG