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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcatcccaaaatacttgcataaaagcatcaactgttatttcaagcttgaaacctgtttttgtgctgtctgttgctcttttgtttaattatttctctgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG

Basic information

species Zea mays
transcript GRMZM2G093359_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093359_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 4
gtgtgcatcccaaaatacttgcataaaagcatcaactgttatttcaagcttgaaacctgtttttgtgctgtctgttgctcttttgtttaattatttctctgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG
   || ||   | | |   | ||||   | |  |  |   |||| |   |||  |    | |        | |||   |  | |  |      ||||||||  ||||||||| ||||| |||||||||||| | ||    |||||||||||||| ||| |||||||||||||||| |||||||||
--atgtattgtaga-tggatacatatgtgtagtatattacattttatttttgtcata-atatccaattgatatgtcaataatgtcctc-----tttctctgccttttagAGGGCAAGGCCATCCAACAGGAGATTCTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATG
















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|149090120|gb|EE179418.2|EE179418
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|149089319|gb|EE178541.2|EE178541
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|149008951|gb|EE041170.2|EE041170
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|12046552|gb|BF728691.1|BF728691
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|78180016|gb|DV550389.1|DV550389
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|6973663|gb|AW438237.1|AW438237
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|149094603|gb|EE180134.2|EE180134
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|101398071|gb|EB820910.1|EB820910
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|31350712|gb|CD435069.1|CD435069
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|31355275|gb|CD439632.1|CD439632
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|71424525|gb|DR806344.1|DR806344
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|149106513|gb|EE188405.2|EE188405
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA
EST: gi|89253028|gb|DY624814.1|DY624814
EST:     GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG                         AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGCCCCTCTCA
genomic: GGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAGgtgtgcatcc ... tgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgtttttgtgctgtctgttgctcttttgtttaattatttctctgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG
                              gtttaat  putative branch site (score: 4)
                                    ttatttctctgttttt  CT-rich tract
                          ttttgtttaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcatcccaaaatacttgcataaaagcatcaactgttatttcaagcttgaaacctgtttttgtgctgtctgttgctcttttgtttaattatttctctgttttttagAGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG