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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcactctctctttgctagtttactgcaggctggtgaatggcctatttcatgtctaaatttcgttatgaatgtggatggttttctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTGGAATTGCCCAGGGGTTAAGATACCTGCACACGGAGCTGCAGCCCCCATT

Basic information

species Zea mays
transcript GRMZM2G119759_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119759_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g58700.1 (Oryza sativa), 3'ss of exon 10
gtaagtca--ctctctctttgctagt--ttactgcaggctggtgaatggcctatttcatgtctaaatttcgttatgaatgtggat--ggttttc------tttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTGGAATTGCCCAGGGGTTAAGATACCTGCACACGGAGCTGCAGCCCCCATT
||||| ||  |||| | ||| ||     |||    | |||     || || |||| ||||| | |  | |   | |  ||   ||  | ||||       ||  || ||||||||| ||||  || || ||||||||||| |||||||| ||||||||||| || || |||||  ||||||||||||| || ||| ||||||| |||||
gtaagccagcctctttattttctgacgattatgtgatgcttagttattgcatattgcatgtgttatgtgcagcaggtttgcttatttgatttttatggggttccttcagATGGAGAAGGAGCTCAGTTATCTTGGCTCAGACGAATGAAAATAGCCATTGGCATCGCGCAGGGTCTAAGATACCTGCATACCGAGTTGCAGCCTCCATT
















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|149107663|gb|EE189542.2|EE189542
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|91050218|gb|EB160636.1|EB160636
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|88746982|gb|DY531123.1|DY531123
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|71770668|gb|DR968605.1|DR968605
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|71313398|gb|DR793250.1|DR793250
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149097230|gb|EE183048.2|EE183048
EST:     CTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: CTAGTCTTCGAGTACGCACCAAATGGGACGTTA-TTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149051626|gb|EE155736.2|EE155736
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|78089519|gb|DV517893.1|DV517893
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|148950050|gb|EC895582.2|EC895582
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|50334832|gb|CO529958.1|CO529958
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|71761155|gb|DR959092.1|DR959092
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|88757283|gb|DY541424.1|DY541424
EST:     GTTAGTCTTCGAGTCCGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|71330749|gb|DR802161.1|DR802161
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149106783|gb|EE188679.2|EE188679
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|101388114|gb|EB816071.1|EB816071
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149013195|gb|EE042830.2|EE042830
EST:     CTAGTCTTCGAGTACGCACCAAATGGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: CTAGTCTTCGAGTACGCACCAAAT-GGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149097302|gb|EE183131.2|EE183131
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|78122547|gb|DV540931.1|DV540931
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|50335669|gb|CO530795.1|CO530795
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|148943639|gb|EC888703.2|EC888703
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|78084470|gb|DV512863.1|DV512863
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149004762|gb|EE039259.2|EE039259
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|86472200|gb|DY238570.1|DY238570
EST:     ACGTTATTTGAGCATTTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: ACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149095721|gb|EE181354.2|EE181354
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|76910133|gb|DV163719.1|DV163719
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|148975399|gb|EE025699.2|EE025699
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|74242567|gb|DT650481.1|DT650481
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTA
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149031687|gb|EE154870.2|EE154870
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149074933|gb|EE163389.2|EE163389
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|94474040|gb|EB702998.1|EB702998
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149089831|gb|EE179109.2|EE179109
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTGCATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|71760111|gb|DR958048.1|DR958048
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|149111973|gb|EE191133.2|EE191133
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|148999085|gb|EE024226.2|EE024226
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
EST: gi|91875214|gb|EB405171.1|EB405171
EST:     GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATT                         ATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG
genomic: GCTAGTCTTCGAGTACGCACCAAATGGGACGTTATTTGAGCATCTACATTgtaagtcact ... ctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcctatttcatgtctaaatttcgttatgaatgtggatggttttctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTGGAATTGCCCAGGGGTTAAGATACCTGCACACGGAGCTGCAGCCCCCATT
             gtctaaa  putative branch site (score: 3)
                                         ttttctttattt  putative PPT
                                         ttttctttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcactctctctttgctagtttactgcaggctggtgaatggcctatttcatgtctaaatttcgttatgaatgtggatggttttctttatttagATGGAGAGGGAGGCCAATTTTCTTGGCTCAGGCGAATGAAGATAGCCATTGGAATTGCCCAGGGGTTAAGATACCTGCACACGGAGCTGCAGCCCCCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG