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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatgttgtgccgctcccatgctatgttgtatcccaagttttatagcatgttttttcaggtatatatatctgaaacttcaaatttgtaaaagtga...

Basic information

species Zea mays
transcript GRMZM2G017086_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 10
TGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatgttg----tgccgctcccatg----ctatgttgtatc-------------ccaagttttatagcatgttttttcaggtatatatatctgaaacttcaaatttgtaaaagtga-----------------------------------------------------
||||||||||||||| |||||  | |||| ||||||||| |||||  | ||||||||||||||||| ||||| ||||| |||||||| ||| |||||||||||||| |||||     |      | |||     |||| || ||||             |  | | | | || ||  ||||| | || || ||   |   |    |   ||| | ||                                                         
TGCAGAAAGTGGTGAAGAGAGTTTAGAGAGAGAATCAGTTTATTCTTTGAAGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGACTTAAGCATgtaagttatgttaccattattaaactcataatttctattttatatcgagtagctcattgctgattctgacaggatagttttttatgtgtacattatttttatactatgcttgcataaaacctcagaatttgtatgagaaggcccatgtaattattcttgtattctttcctgcag

upper sequence: GRMZM2G017086_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT1G51710.1 (Arabidopsis thaliana), 5'ss of exon 9
TGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatgttgtgccgctcccatgctatgttgtatcccaagttttatagcatgttttttcaggtatatatatc-tgaaacttcaaatttgtaaaagtga----------------------------------------------------------
|  ||||||||| || || |||   ||||||||||| |||||||| || || ||||||||||| || || ||||||||  | ||||| ||| | || ||||| || ||  ||       | ||||  ||   | | |  |   ||||  ||||||||| | | | || | | |   |   ||  |   ||||  | | |                                                            
TCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGATTAAAACATgtgagcaactttt--ataattccattatagactttgtttctgatttttcagcatgtttct-cggatacaaaaaaaataggacagcg--tttgctatattctgcttattataaattttttttttttgatgaacggcttcaatttttctggtttactgaag
















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|32934266|gb|CF039078.1|CF039078
EST:     AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCAT                         GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
genomic: AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatg ... ctttgtacagGGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
EST: gi|32866635|gb|CF006317.1|CF006317
EST:     AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCAT                         GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
genomic: AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatg ... ctttgtacagGGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
EST: gi|12968043|gb|BG264990.1|BG264990
EST:     GTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCAT                         GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
genomic: GTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatg ... ctttgtacagGGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
EST: gi|32932531|gb|CF037343.1|CF037343
EST:     AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCAT                         GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
genomic: AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatg ... ctttgtacagGGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
EST: gi|211437528|gb|FK975648.1|FK975648
EST:     AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCAT                         GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
genomic: AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatg ... ctttgtacagGGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
EST: gi|32930082|gb|CF034894.1|CF034894
EST:     AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCAT                         GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
genomic: AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatg ... ctttgtacagGGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
EST: gi|32945380|gb|CF050199.1|CF050199
EST:     AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCAT                         AAAATGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
genomic: AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatg ... ctttgtacagGGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
EST: gi|32932473|gb|CF037285.1|CF037285
EST:     AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCAT                         GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
genomic: AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatg ... ctttgtacagGGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
EST: gi|32931528|gb|CF036340.1|CF036340
EST:     AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCAT                         GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
genomic: AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatg ... ctttgtacagGGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCA
EST: gi|67017287|gb|CO446036.1|CO446036
EST:     AGTGTCATATATCTCAAGATGTGAACCATCNTCATGAGGGAATTAAGCAT                         GGCTTNGA-GACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGC
genomic: AGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatg ... ctttgtacagGGCTT-GAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGAATTAAGCATgtaagtaatgttgtgccgctcccatgctatgttgtatcccaagttttatagcatgttttttcaggtatatatatctgaaacttcaaatttgtaaaagtga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG