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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggatatttaggcgtttccattggattgatttttacttactagccacctaccgttctcctaacaatgttctaacattttctaacattatcatttttgaagATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG

Basic information

species Zea mays
transcript GRMZM2G107867_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107867_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 6
-gggatatttaggcgtttccattggattgatttttacttact-agccacctaccgttctcctaacaatgttctaacattttctaacattatcatttttgaagATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG
   ||||  |   |  || || |  ||   || |||| |  |        ||   || || |  || | | |||| || ||   | || | | | ||||||||||||||||||||| |||| ||| ||||| ||  |||| | | | ||| |||||||||||||||| ||| |||  ||||| |||||||||
gcagataagttttcacttgcaat--atcacttattacatgtttgattttttataattatcttgccactttgctaatatcttgatatatgaccttctttgaagATTGATGAAGATACCCTTCAAGACGTTGTAAACTTGGGTTATGAAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAAAATGAG

upper sequence: GRMZM2G107867_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 6
-gggatatttaggcgtttccattggattgatttttacttactagccacctacc--gttctcctaacaatgttctaacattttctaacattatcatttttgaagATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG
 |  ||||  |    ||| |||  | | |||||||  |   || |   |      | |||| |  ||||| | |||  ||||   | ||   | ||||||||||||||||||||||| |||| |||||| || ||  |||| | |   ||| |||||||||||||||| ||| |||  ||||| || ||||||
tgcaatatc-acttatttacat--gttcgattttttatagttatctttccgtttagctctcgtggcaatggtataatgttttgatatatggccttttttgaagATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG
















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:     CACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATG                         ATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAAC
genomic: CACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATGgtatgtcctc ... atttttgaagATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAAC
EST: gi|60341419|gb|DN208392.1|DN208392
EST:     CACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATG                         ATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAAC
genomic: CACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATGgtatgtcctc ... atttttgaagATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAAC
EST: gi|91872727|gb|EB402684.1|EB402684
EST:     CACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATG                         ATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAAC
genomic: CACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATGgtatgtcctc ... atttttgaagATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAAC
EST: gi|32930411|gb|CF035223.1|CF035223
EST:     CACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATG                         ATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAAC
genomic: CACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATGgtatgtcctc ... atttttgaagATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAAC
EST: gi|211186173|gb|FL452294.1|FL452294
EST:     CAAGCCAAAAATG                         ATTGATGAAGATACACTTCGAGATG-TGTTTAATATGGGATTTACCAAGA
genomic: CAAGCC-AAAATGgtatgtcctc ... atttttgaagATTGATGAAGATACACTTCGAGATGTTG-TTAATATGGGATTTAACAAGA
EST: gi|211440538|gb|FL230375.1|FL230375
EST:     CACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATG                         ATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAAC
genomic: CACGTTACTTGGCAGTGCCTCCACCAGATACGACACAACAAGCCAAAATGgtatgtcctc ... atttttgaagATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctaccgttctcctaacaatgttctaacattttctaacattatcatttttgaagATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG
                                ttctaac  putative branch site (score: 1)
                                           tcattttt  putative PPT
                             attttctaacattatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggatatttaggcgtttccattggattgatttttacttactagccacctaccgttctcctaacaatgttctaacattttctaacattatcatttttgaagATTGATGAAGATACACTTCGAGATGTTGTTAATATGGGATTTAACAAGAACCATGTGTGTGAATCACTGTGCAGCAGACTTCAAAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC