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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGATAGCTTAAGCGTAATGCATCCTGAAGCCAACAGATCTGTTGCACCGGTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgttctttttggatgttatatcaatatcccatacttttttcaacatatttaaacccacgtgaccgagcaaagttccctttagtccttattgaa...

Basic information

species Oryza sativa
transcript LOC_Os01g58740.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g58740.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 5
AGGATAGCTTAAGCGTAATGCATCCTGAAGCCAACAGATCTGTTGCACCGGTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgttctttttggatgttatatcaatatcccatacttttttcaacatatttaaacccacgtgaccgagcaaagttccct-ttagtccttattgaa
||||||||||||| || |||||||| |||||||||||||||||||| ||||||||||||||||| ||||| || |||||  | |  ||| |||||| |||||||| |  |          |   |||       ||  |  | |||||| | |||| |     | |  |   | | |  || |       | | ||  || 
AGGATAGCTTAAGTGTCATGCATCCAGAAGCCAACAGATCTGTTGCGCCGGTTGAGATGTGCCCGATCCTAAAAGCACTACATAGGATTCTGATCACGAGgttagaacctaagaccaacgtcacatactctacaccagttatattttcagcgtatt-acctatatgccagtaacctatattactaacccatacataccgat
















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|86537385|gb|CI177591.1|CI177591
EST:     CCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAG                         GGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
genomic: CCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgt ... gtatttacagGGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
EST: gi|86537374|gb|CI177580.1|CI177580
EST:     GAAGGCACTGTACAAAATTTTGATCAAGAG                         GGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
genomic: GAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgt ... gtatttacagGGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
EST: gi|86493591|gb|CI136224.1|CI136224
EST:     GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAG                         GGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
genomic: GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgt ... gtatttacagGGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
EST: gi|86487645|gb|CI130278.1|CI130278
EST:     GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAG                         GGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
genomic: GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgt ... gtatttacagGGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
EST: gi|86537396|gb|CI177602.1|CI177602
EST:     GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAG                         GGAACTTCCTCCGTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGT
genomic: GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgt ... gtatttacagGGAACTTCCTCC-TGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGT
EST: gi|89177422|gb|CI250871.1|CI250871
EST:     GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAG                         GGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
genomic: GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgt ... gtatttacagGGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
EST: gi|86831660|gb|CI301510.1|CI301510
EST:     GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAG                         GGAACTTCCTCCTGATTCGACCCTTCAGGCCATAAGAGATGAAACAATGTA
genomic: GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgt ... gtatttacagGGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
EST: gi|88902622|gb|CI088160.1|CI088160
EST:     GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAG                         GGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA
genomic: GTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgt ... gtatttacagGGAACTTCCTCCTGATTCGATCCTTCAGGCCATAAGAGATGAAACAATGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGATAGCTTAAGCGTAATGCATCCTGAAGCCAACAGATCTGTTGCACCGGTTGAGATGTGCCCAATCCTGAAGGCACTGTACAAAATTTTGATCAAGAGgttagtatgttctttttggatgttatatcaatatcccatacttttttcaacatatttaaacccacgtgaccgagcaaagttccctttagtccttattgaa

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG