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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttcgcctgatcattattttccgcttcacctttaccatttaatataaaccactagcattgtattacattctcttttttccttgaccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGGCTTCCGGAAACTAGCAGAGCCGCTTCCATTCTCCAAGCAGCACCATTCA

Basic information

species Oryza sativa
transcript LOC_Os05g06760.2
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G177026_T02 (Zea mays), 3'ss of exon 5
gtatcctt-cgcctgatca--ttattttccgcttca--cctttaccatttaa-tataaaccactagcattgtatt-------acattctcttttttccttgaccatc-att---agATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGGCTTCCGGAAACTAGCAGAGCCGCTTCCATTCTCCAAGCAGCACCATTCA
|||||||  |   || |    ||| |||   ||     | ||||    | || || |     |||| ||| | ||         || || | || |||||||||||  |||   || |||||||  || |||| ||| ||||||||||||||||| || |||   |||||| |||||||||| ||||| || || ||||| || |||||||| || 
gtatcctcgcatgtgtttcacttacttttgtctatggtcttttattgctaaaatacagtttgctagtattatttttgttatggtatcctgtattgtccttgaccatttatttaaagGTTCTGCTCTGAGGGTAGCTGTCCCAAAGAAGACCCCTTGTCTCTGGAGGGCTTCAGGAAACTAGCCGAGCCTCTGCCCTTCTCTAAACAGCACCACTCG
















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|287145|gb|D15950.1|D15950
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|58679080|gb|CK067767.1|CK067767
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTTTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGA
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatataaaccactagcattgtattacattctcttttttccttgaccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGGCTTCCGGAAACTAGCAGAGCCGCTTCCATTCTCCAAGCAGCACCATTCA
 ttccttgac  putative branch site 
                            ttctcttttttccttg  putative PPT
                 attgtatta  TA-rich tract