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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggacatgcattgtgagccttatatgttccttttggtgacttgtttactaaatttttgaaaactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG

Basic information

species Zea mays
transcript GRMZM2G107867_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 7
gtatggacatgcattgtgagccttatatgttccttttggtgacttgtttactaaatttttgaaaactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG
||||   || |||   ||| |  | |   | | ||||  | |     || || | |||| ||  | |||  |||||||||||||||||||||| |||||||||||||| ||  |||| || ||||||||||| || ||||| |||||||||||| ||
gtatatgcaagcaa-atgaac--tgttcatcctttttaattatcatattgctga-ttttagaccattttccagGCAACTGTTGCATATTATTTGCTATTGGACAATCGATTCCGAGCTACCAGTGGCTATCTGGGAGCAGACTATCAAGAATCATTG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 7
gtatggacatgcattgtgagccttatatgttccttttggtgacttgtttactaaatttttgaaaactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG
||||   ||  ||   ||| |  | |   | | ||||  |||     || || | |||| ||  | ||| |||||||||||||||||||||||||| ||||||||||| ||  |||| || ||||||||| | || ||||| |||||||||||  ||
gtatatgcaaacaa-atgaac--tgttcatcctttttaatgatcacattgctga-ttttagaccattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG
















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|18661445|gb|BM501401.1|BM501401
EST:     TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG                         GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
genomic: TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAGgtatggacat ... aactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
EST: gi|60341419|gb|DN208392.1|DN208392
EST:     TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG                         GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
genomic: TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAGgtatggacat ... aactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
EST: gi|91872727|gb|EB402684.1|EB402684
EST:     TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG                         GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
genomic: TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAGgtatggacat ... aactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
EST: gi|32930411|gb|CF035223.1|CF035223
EST:     TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG                         GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
genomic: TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAGgtatggacat ... aactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
EST: gi|211210980|gb|FL114022.1|FL114022
EST:     TAACAAGAACCAT-TGTGTGAATCACTGTGCAGCAGACTTTAAAATGAG                         GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
genomic: TAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAGgtatggacat ... aactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
EST: gi|211186173|gb|FL452294.1|FL452294
EST:     TTACCAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG                         GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
genomic: TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAGgtatggacat ... aactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGT
EST: gi|211440538|gb|FL230375.1|FL230375
EST:     TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG                         GCAACTGTTGCATATTATTTACTATTGGGACAATCGGTTTAGAGCAACTAG
genomic: TTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAGgtatggacat ... aactttgtagGCAACTGTTGCATATTATTTACTATTGG-ACAATCGGTTTAGAGCAACTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccttatatgttccttttggtgacttgtttactaaatttttgaaaactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG
                              tactaaa  putative branch site (score: 1)
                            tttactaaatttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggacatgcattgtgagccttatatgttccttttggtgacttgtttactaaatttttgaaaactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT