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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgagactgcgtacacctgatgcctgcatcctggtagtggtacacagacagaacattttagtttctttttttgtctgaacttgtcctcgcccggccaatgaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTACGCCATCCTGGCCAACAAGGAGGTGATCGCCGTCAACCAAG

Basic information

species Zea mays
transcript GRMZM2G095126_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095126_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g35070.1 (Oryza sativa), 3'ss of exon 11
gtcagtgagactgcgtacacctgatgcctgcatcctggtagtggtacacagacagaacattttagtttctttttttgtctgaacttgtc---ctcgcccggccaatgaac-gcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTACGCCATCCTGGCCAACAAGGAGGTGATCGCCGTCAACCAAG
                  |  |  || |   |        ||| || ||  ||    | ||  | | |  |  | |  |||   ||| |             |  ||||  |  ||||| ||||| |||||||| |||||||| ||||||||||||| ||||||||||| ||||||||||||||||||||| ||||||||||||||||
----------------ctatatcgtgaccagaaaagaacggtgatatact-actctgctttgcattattctgctcttgctgggtttgacagatcgaaattttctctgaattggtcagGCTCCTCTGATCATCGGGTGCGACGTGAGGCACATGTCGCAGGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG
















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|71323535|gb|DR798428.1|DR798428
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|88753305|gb|DY537446.1|DY537446
EST:     GGCCCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|94473544|gb|EB702502.1|EB702502
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGGGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|148929477|gb|EC875592.2|EC875592
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGTTGCGACGTCAGGCACATGTCGCGGGAGAGGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|5740192|gb|AI947882.1|AI947882
EST:     TGACCAACAGCGAGTCCTTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCCCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|149080680|gb|EE169738.2|EE169738
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|211321684|gb|FL295978.1|FL295978
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|71767715|gb|DR965652.1|DR965652
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttagtttctttttttgtctgaacttgtcctcgcccggccaatgaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTACGCCATCCTGGCCAACAAGGAGGTGATCGCCGTCAACCAAG
       tttcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgagactgcgtacacctgatgcctgcatcctggtagtggtacacagacagaacattttagtttctttttttgtctgaacttgtcctcgcccggccaatgaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTACGCCATCCTGGCCAACAAGGAGGTGATCGCCGTCAACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG