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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtctgaagggttaaattatgcttgctagtaaatgtcgagacatttgattttttttcatgccggtaagtgatgagtccaatattttctttcctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATACGCAGCGGAGCATCTTGCAATCTCAGTCTTCAACAAGGGTCAAAAATAC

Basic information

species Zea mays
transcript GRMZM2G166903_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166903_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g41520.1 (Oryza sativa), 3'ss of exon 9
----------------------------------------------cgtctgaagggttaaattatgcttgctagt-aaatgtcgagacatttgattttttttcatgccg-gtaagtgatgagt-ccaatattttctttcctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATACGCAGCGGAGCATCTTGCAATCTCAGTCTTCAACAAGGGTCAAAAATAC
                                                 |||      |||  | |   | ||  | |  || |   |  ||| | || |    |    | | |  | |  | | |   | | ||||||||||||||||||| || || ||||| || |||||  | ||| ||||||| ||||||||||||||  |||||||||| || ||||| | |||   ||| || |||| | | 
gtaagatagggggtggttcattgtctacttttcttcattttgaaggaaactggcaaaataatctgtagctactgttcagctggctccatttttaacttctcaaaacagtgtgaacctaacaaattctgttgtgttctttcctttggcagGCTTGGGTTGATGGTAGCAGGTGGCGTGGTGTTGGCATCGTTTATGACATACGCTTCGGAGCATCTAGCTATCTCGGCCTTTGTCAAAGGCCAAAGAGAT
















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|211424146|gb|FL418433.1|FL418433
EST:     ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAA                         GCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
genomic: ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAAgtaaggcacc ... cctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
EST: gi|149085754|gb|EE175274.2|EE175274
EST:     ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAA                         GCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
genomic: ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAAgtaaggcacc ... cctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
EST: gi|89760627|gb|DY688959.1|DY688959
EST:     ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAA                         GCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
genomic: ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAAgtaaggcacc ... cctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
EST: gi|78021391|gb|DV489778.1|DV489778
EST:     ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAA                         GCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
genomic: ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAAgtaaggcacc ... cctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
EST: gi|60395150|gb|DN228019.1|DN228019
EST:     ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAA                         GCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
genomic: ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAAgtaaggcacc ... cctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
EST: gi|211402880|gb|FL375611.1|FL375611
EST:     ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAA                         GCTAGGATTAATGGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACAT
genomic: ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAAgtaaggcacc ... cctttggcagGCTAGGATTAATGG-TCGCTGGTGGTATTGTGCTGGCATCTTTTATGACAT
EST: gi|6020784|gb|AW065712.1|AW065712
EST:     ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAA                         GCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
genomic: ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAAgtaaggcacc ... cctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
EST: gi|149094689|gb|EE180238.2|EE180238
EST:     ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAA                         GCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
genomic: ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAAgtaaggcacc ... cctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
EST: gi|5871116|gb|AW017557.1|AW017557
EST:     ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAA                         GCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
genomic: ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAAgtaaggcacc ... cctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
EST: gi|110200546|gb|EC882443.1|EC882443
EST:     ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAA                         GCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA
genomic: ATTACTGTACTGTTACCGACTATCTTGGGCATAACTGCATTGTTCACAAAgtaaggcacc ... cctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattttttttcatgccggtaagtgatgagtccaatattttctttcctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATACGCAGCGGAGCATCTTGCAATCTCAGTCTTCAACAAGGGTCAAAAATAC
 atttgat  putative branch site (score: 5)
                                   tattttctttccttt  putative PPT
                                 aatattttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtctgaagggttaaattatgcttgctagtaaatgtcgagacatttgattttttttcatgccggtaagtgatgagtccaatattttctttcctttggcagGCTAGGATTAATGGTCGCTGGTGGTATTGTGCTGGCATCTTTTATGACATACGCAGCGGAGCATCTTGCAATCTCAGTCTTCAACAAGGGTCAAAAATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA