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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaacgagattgcccttttcatgctagattttcacgttgccatgccaccctatttccaatctcttataactacaagcaatgagattacaattttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAATTATAACTTTGATCATCCAG

Basic information

species Zea mays
transcript GRMZM2G169462_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 3
gcaacgagattgcccttttcatgctagattttc--acgttgccatg---ccaccctatttccaatctcttataactacaagcaatgagattacaattttt---tgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAATTATAACTTTGATCATCCAG
      | |||    | | | ||||  |||     ||      |||   || |  |||    ||| || |||  |  | |  | |  | ||||||| |||   |||||||||| ||||||||||| ||| | ||||| ||||| || ||||| ||| |||||||||||||||||||||
------aaattagtatat-cgtgctgtattgctagacaccagaatgtgccccctttatgctaaatatcatattgccgcca-tattttgtttacaatctttctttgcagGAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 3
---gcaacgagattgcccttttcatgctagatt-ttcacgttgccatgccaccctatttccaatctcttataactacaagcaatgagattacaatttt---ttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAATTATAACTTTGATCATCCAG
   ||           | ||    |   ||||| | || ||||  ||  ||  |||     ||| ||  ||     ||     ||   || | |||||   ||||||||||||||||||||||| ||  | ||||| ||||| || ||||| ||| |||||||||||||||||||||
taggcttttctgcaaacattccagttacagattgtacaagttggtatatcatgcta-----aatgtcacattggggcatatgttgt--ttccgattttgcattgcagGAGTCCTTTTATTATGGGTTATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG
















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|78107197|gb|DV525615.1|DV525615
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|211396287|gb|FK980044.1|FK980044
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|4609834|gb|AI600673.1|AI600673
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|211393676|gb|FK980040.1|FK980040
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAAATAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|71439100|gb|DR820150.1|DR820150
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|211396286|gb|FK980043.1|FK980043
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|148987214|gb|EE031046.2|EE031046
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|211393675|gb|FK980039.1|FK980039
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTC-TTTTATTATGGATTGACGGATGA
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGA
EST: gi|211396292|gb|FK980049.1|FK980049
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|211396289|gb|FK980046.1|FK980046
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|211396291|gb|FK980048.1|FK980048
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|211393673|gb|FK980037.1|FK980037
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|211396288|gb|FK980045.1|FK980045
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAAT
EST: gi|211393674|gb|FK980038.1|FK980038
EST:     AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG                         GAGTCCTTTTATTATGGATTGACGGGATGAAGAATTAGTACATGTCCATAA
genomic: AGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAGgtttgtgcat ... ttttttgcagGAGTCCTTTTATTATGGATTGACGG-ATGAAGAATTAGTACATGTCCATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccctatttccaatctcttataactacaagcaatgagattacaattttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAATTATAACTTTGATCATCCAG
                  ttataac  putative branch site (score: 2)
                                             ttttttgc  putative PPT
                                    agattacaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaacgagattgcccttttcatgctagattttcacgttgccatgccaccctatttccaatctcttataactacaagcaatgagattacaattttttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAATTATAACTTTGATCATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - tgccctt
- - - - - - - - -ttcatgc
- - - - - - - - - - - - - - - - - - - -ccatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagcaa