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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgccaatacattccatttgactcatttgatggtttacagtgtttcctgaaaacttagtgacgtggaattctttttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT

Basic information

species Zea mays
transcript GRMZM2G492252_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G492252_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16570.2 (Oryza sativa), 3'ss of exon 5
---gtgtgcca-atacattccatttgactcatttgatggtttacagtgtttcctgaaaacttagtgacgtggaattctttttgttt-cagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT
| | || || | || | |||| | || || | | ||||| || | | || | ||||| || |||||||||| | || || || ||||||| |||||||||| |||| |||||| ||||||||||||||||||||| |||||||||| |||||||| || ||
gtgatacactttattcacttaggttaattcatatactgcttcttact--ctcctgcaagcattacattgtagctgatgttttgcttgcagATTATGATGCCCTTAGGGCCTTGGATGCAGACAATAGCCCTCATGCTCCTTCGATGAGTGAAGAAGAAATAAATGCTCTTCCTGTATTCAAATACAAGGT
















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|78074674|gb|DV503108.1|DV503108
EST:     CCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: CCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|60359234|gb|DN226207.1|DN226207
EST:     GACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|78123225|gb|DV541609.1|DV541609
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|71448720|gb|DR829770.1|DR829770
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|110517661|gb|EE022248.1|EE022248
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|88758240|gb|DY542381.1|DY542381
EST:     AGACTTCAACTGGCTCTTTTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCGGACAATAGCCTGCATGTTCCTT
genomic: AGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|71774881|gb|DR972759.1|DR972759
EST:     AGCCTTAGACTTCAACT-GCTTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: AGCCTTAGACTTCAACTGGC-TCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|60352872|gb|DN219845.1|DN219845
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|86467860|gb|DY234230.1|DY234230
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggtttacagtgtttcctgaaaacttagtgacgtggaattctttttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT
 atttgat  putative branch site (score: 5)
 ttctttttgtttc  putative PPT
 aattctttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgccaatacattccatttgactcatttgatggtttacagtgtttcctgaaaacttagtgacgtggaattctttttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA