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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgatatgtttgacatttttgtaaaatttccttagcctactttatatggaatgttcattgtcaaaaatgtggttcgtacattctaattcctctttagAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAAGGATGCCTGGGATCCACAGAACCGGGGAAGGGCATAATCAATTCTGGGT

Basic information

species Zea mays
transcript GRMZM2G085747_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 9
gtatctgatatgtttgacatttttgtaaaatttccttagcctactttatatggaatgttcattgtcaaaaatgtggttcgtacattctaattcctctttagAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAAGGATGCCTGGGATCCACAGAACCGGGGAAGGGCATAATCAATTCTGGGT-------
|||| |||||||||||| || ||| | || | || || || ||| | || ||||||||| | || ||| | | |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||| |||||||||| ||||| |||| | |||||||||||||||||||||||||||
gtatatgatatgtttgatatgcttgcatttttctatcagtttatttcatacaaggtatttcttgtcaaaagtctgtttcctccgttctaattcctctttagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGAC
















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|30087213|gb|CB885421.1|CB885421
EST:     CCTCTCCAGGATTTTACGAATCAAAAGATAGTCGTTGTGGGAGCTGGAAG                         --T---G--CTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAA
genomic: CCTCTCCAGGATTTTACGAATCAAAAGATAGTCGTTGTGGGAGCTGGAAGgtatctgata ... tcctctttagAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAA
EST: gi|32850587|gb|CD990268.1|CD990268
EST:     CCTCTCCAGGATTTTACGAATCAAAAGATAGTCGTTGTGGGAGCT-G--G                         -A---AGTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAA
genomic: CCTCTCCAGGATTTTACGAATCAAAAGATAGTCGTTGTGGGAGCTGGAAGgtatctgata ... tcctctttagAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAA
EST: gi|74232917|gb|DT640831.1|DT640831
EST:     AAAGATAGTCGTTGTGGGAGCTGGAAG                         AATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAA
genomic: AAAGATAGTCGTTGTGGGAGCTGGAAGgtatctgata ... tcctctttagAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatggaatgttcattgtcaaaaatgtggttcgtacattctaattcctctttagAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAAGGATGCCTGGGATCCACAGAACCGGGGAAGGGCATAATCAATTCTGGGT
                                      ttctaat  putative branch site (score: 2)
 ttctaattcctcttt  CT-rich tract
 attctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgatatgtttgacatttttgtaaaatttccttagcctactttatatggaatgttcattgtcaaaaatgtggttcgtacattctaattcctctttagAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAAGGATGCCTGGGATCCACAGAACCGGGGAAGGGCATAATCAATTCTGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG