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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatatatacaccacatacaaattattatcatgcaccctgctttcgttcactctagcttcatcactcatcgtggtaactctgttgggatgaatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCCCAGTTACTGGATGCAGACGCTTTTCCGCGAGTCTAGTGGTGCTATGTTC

Basic information

species Zea mays
transcript GRMZM2G077299_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 14
ccatatatacaccacatacaaattattatcatgcaccctgctttcgttcactctagcttcatcactcatcgtggtaactctgttgggatgaatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCCCAGTTACTGGATGCAGACGCTTTTCCGCGAGTCTAGTGGTGCTATGTTC
             |  |   |  |     ||||    ||   || ||    | | | ||  | |   |     ||||   || |   || || |||||||||||||||||||||| || || || ||||||||||| || ||||| ||||| ||||||||||||||||| |||||||| || ||||| ||||||||||| 
----------gttagttttga--tggctccatggtttctttatttgt--gtttttgtttatttaacaagtactgtaataatgcttcaatcaaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCCTAGTTACTGGATGCAGACTCTTTTCCGTGAATCTAGCGGTGCTATGTTT

upper sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 15
ccatatatacaccacatacaaattattatcatgcaccctgctttcgttcactctagcttcatcactcatcgtggtaactctgttgggatgaatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCCCAGTTACTGGATGCAGACGCTTTTCCGCGAGTCTAGTGGTGCTATGTTC
             |  |    || | |  ||||    ||   || ||    | | | ||  | |   |     ||||   || |   || || |||||||||||||||||||||| || || || ||||||||||| || || || ||||| ||||||||||||||||| |||||| | || ||||| ||||||||||| 
----------gtta-gttttgatgact-ccatggtttctttatttgt--gtttttgtttatttaacaagtactgtaataatgcttcaatcaaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCCTAGTTACTGGATGCAGACTCTTTTCGGTGAATCTAGCGGTGCTATGTTT
















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|32832928|gb|CD972606.1|CD972606
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32915958|gb|CF020770.1|CF020770
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|213170538|gb|FM181869.1|FM181869
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|116814377|gb|EC856917.1|EC856917
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32834805|gb|CD974483.1|CD974483
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32838656|gb|CD978334.1|CD978334
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32846404|gb|CD986085.1|CD986085
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32834343|gb|CD974021.1|CD974021
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32915959|gb|CF020771.1|CF020771
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32847114|gb|CD986795.1|CD986795
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32836113|gb|CD975791.1|CD975791
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32846779|gb|CD986460.1|CD986460
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32833806|gb|CD973484.1|CD973484
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32846254|gb|CD985935.1|CD985935
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32865761|gb|CF005443.1|CF005443
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32833276|gb|CD972954.1|CD972954
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCC
EST: gi|32847472|gb|CD987153.1|CD987153
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|74232032|gb|DT639946.1|DT639946
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32846575|gb|CD986256.1|CD986256
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32839169|gb|CD978850.1|CD978850
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTATTCAACTTCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|17970148|gb|BM276913.1|BM276913
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|71769432|gb|DR967369.1|DR967369
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32847067|gb|CD986748.1|CD986748
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACCCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32833492|gb|CD973170.1|CD973170
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|22489289|gb|BU049212.1|BU049212
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|71441725|gb|DR822775.1|DR822775
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGAAACC-AGACGCAAT
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAAT
EST: gi|32833419|gb|CD973097.1|CD973097
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32847159|gb|CD986840.1|CD986840
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32832289|gb|CD971967.1|CD971967
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32834130|gb|CD973808.1|CD973808
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32847619|gb|CD987300.1|CD987300
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32833120|gb|CD972798.1|CD972798
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGC
EST: gi|32847167|gb|CD986848.1|CD986848
EST:     GCTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32847649|gb|CD987330.1|CD987330
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32846820|gb|CD986501.1|CD986501
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
EST: gi|32832861|gb|CD972539.1|CD972539
EST:     GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGAC                         GTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC
genomic: GTTTCCATGGCAAGTTACGCGCCACTATTCGTAAACGACAATGACCAGACgttagtacat ... aatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcactctagcttcatcactcatcgtggtaactctgttgggatgaatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCCCAGTTACTGGATGCAGACGCTTTTCCGCGAGTCTAGTGGTGCTATGTTC
                          tggtaac  putative branch site (score: 2)
                                             aatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatatatacaccacatacaaattattatcatgcaccctgctttcgttcactctagcttcatcactcatcgtggtaactctgttgggatgaatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCCCAGTTACTGGATGCAGACGCTTTTCCGCGAGTCTAGTGGTGCTATGTTC

- - - - -caccaca
- - - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgg