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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgggatattcacgcggagaatgagttgtctctgtatggttctcgatgtaaatttgaagcagaaaacttttttttttgcgtacttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTTGAGGAGATGGATGCTGACTAAGAAACAGGACGATTTGCCCAGACTTGGT

Basic information

species Zea mays
transcript GRMZM2G130398_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130398_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 10
gtactgggatattcacgcggagaatgagttgtctctgtatggttctcgatgtaaatttgaagcagaaaacttttttttttgcgtact-tgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTTGAGGAGATGGATGCTGACTAAGAAACAGGACGATT-TGCCCAGACTTGGT
||  |  | | ||       | ||| | |   ||||||     | |   ||| || ||            |  |   || || ||||   ||||||||||   ||| || |||||||||||||| | ||| ||||||||||| |||||||||||||||||||| |||||       ||| | ||  |    || | 
gtgttctgttgttattt--aaaaataaataaactctgtccatatttt--tgtgaactt------------tgctcacttggcatactgcatacagGTTCCTGCTGATCTTTTGGAGCAGGCCAAGGTTGCAGCTCAGGCAGCGCTTGAGGAGATGGATGCTGATTAAGAGGAGACCCGACTATGTTCTACGTTTG-
















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|166504674|gb|EG292604.1|EG292604
EST:     ATGAATCGAACCGTCAGCATCAGAAG                         GTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: ATGAATCGAACCGCCAGCATCAGAAGgtactgggat ... acttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
EST: gi|32832322|gb|CD972000.1|CD972000
EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtactgggat ... acttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCT
EST: gi|31353269|gb|CD437626.1|CD437626
EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGTCAGCATCAGAAG                         GGTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtactgggat ... acttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
EST: gi|148983025|gb|EE028929.2|EE028929
EST:     GT-GGAGTTGAGCTGGATCTGTGATGAATCGAACCCGC-AGCATCAGAAG                         GTTCCAAATGA
genomic: GTTGGAGTTGAGCTGGATCTGTGATGAATCGAACC-GCCAGCATCAGAAGgtactgggat ... acttgtacagGTTCCAAATGA
EST: gi|76280505|gb|DV020073.1|DV020073
EST:     GTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCCGC-AGCATCAGAAA                         GTTCAAAATGAACTGTTGGAGCAGGCCAAAGCTGCT
genomic: GTTGGAGTTGAGCTGGATCTGTGATGAATCGAACC-GCCAGCATCAGAAGgtactgggat ... acttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCT
EST: gi|32795302|gb|CD947538.1|CD947538
EST:     GATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: GATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtactgggat ... acttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
EST: gi|60351410|gb|DN218383.1|DN218383
EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGTCAGCATCAGAAG                         GTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtactgggat ... acttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
EST: gi|32834256|gb|CD973934.1|CD973934
EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtactgggat ... acttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
EST: gi|148949400|gb|EC894857.2|EC894857
EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtactgggat ... acttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttctcgatgtaaatttgaagcagaaaacttttttttttgcgtacttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTTGAGGAGATGGATGCTGACTAAGAAACAGGACGATTTGCCCAGACTTGGT
                        agaaaacttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgggatattcacgcggagaatgagttgtctctgtatggttctcgatgtaaatttgaagcagaaaacttttttttttgcgtacttgtacagGTTCCAAATGAACTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTTGAGGAGATGGATGCTGACTAAGAAACAGGACGATTTGCCCAGACTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA