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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccagcctaccctcacttttttatattcctttatctgcttgatatatactgagacctagttgcttgatatatactgagacctagttttctctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTGGCTGAATTCTACGAAGAGTGGAGTGGCAGGGCTTGAGGTTGAACAACCA

Basic information

species Zea mays
transcript GRMZM2G459291_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G459291_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g34470.1 (Oryza sativa), 3'ss of exon 6
-----cccagcctaccctcacttttttatattcctttatctgcttgatatatactgagacctagttgcttgatatatactgagacctagttttctctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTGGCTGAATTCTACGAAGAGTGGAGTGGCAGGGCTTGAGGTTGAACAACCA
        | | |   |||   |||   || | |      | ||||    || |    | ||  |   |||   |    ||| ||| | ||  || || |||||||||||||||| |||||| ||||||||||| | |||||||||||| ||||||||||||||||| ||||||||||||||||| |||||| ||||| ||||||
atcttaataccatgtactccaatttacctagtacaaacattccttgtagaatcccattatctcttcctttggcgt----tgacacc-atttcactttgtgcatagGCCGGGAAAAAGAGAGCAGAGAAAAGGCACAAGTTCATGGAGGACTTTGTGGCTGAATTCTATGAAGAGTGGAGTGGCAGAGCTTGAAGTTGACCAACCA

upper sequence: GRMZM2G459291_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G02920.1 (Glycine max), 3'ss of exon 5
------------------------------------cccagcctaccctcacttttttatattcctttatct--gcttgatatatactg-agacctagttgcttgatatatactgagacctagttttct----ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTGGCTGAATTCTACGAAGAGTGGAGTGGCAGGGCTTGAGGTTGAACAACCA------
                                         |  |  |  |  | |  || ||  ||| |    |  ||  |   | |  |  |||   |  |  || | |  ||  |  |   | ||     |  |    |||| ||||||||||| || |||| |||||||| |||||||||||| ||||||   || |||||||| || |||| |||      || | | | |  |||||      
gtaggctatattactatttggctgaaatgatcaaattttgacgaagaccaaagtgtgcatttttttttgttaaagtctgtcaagaagtatatgcctgtgtattaaatctgtcatggaatttgaatctcaactacctatttcagGCTGGGAAAAGGAGGGCAGAGAGAAGGCATAAGTTCATGGAGGAGTTTGTGAAAGAGTTCTACGACGAATGGAATGG------TTTAAGCTAATAAACCATTCCAC
















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|60348894|gb|DN215867.1|DN215867
EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGGGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
EST: gi|60354947|gb|DN221920.1|DN221920
EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
EST: gi|74239921|gb|DT647835.1|DT647835
EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGG-ATAGGTTCATGGAGGAA
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAA
EST: gi|76018399|gb|DT945569.1|DT945569
EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
EST: gi|78021401|gb|DV489788.1|DV489788
EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
EST: gi|6227239|gb|AW155838.1|AW155838
EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
EST: gi|148945620|gb|EC890877.2|EC890877
EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
EST: gi|60359077|gb|DN226050.1|DN226050
EST:     AAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: AAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactgagacctagttgcttgatatatactgagacctagttttctctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTGGCTGAATTCTACGAAGAGTGGAGTGGCAGGGCTTGAGGTTGAACAACCA
                gcttgat  putative branch site (score: 5)
                                       ttttctct  putative PPT
                  ttgatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccagcctaccctcacttttttatattcctttatctgcttgatatatactgagacctagttgcttgatatatactgagacctagttttctctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTGGCTGAATTCTACGAAGAGTGGAGTGGCAGGGCTTGAGGTTGAACAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG