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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactaaccattatatgggaattgtgtttcagctacactcgatatattgcttctttttctcctttcgatccattataaacctgagtactagttgttgcattacctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG

Basic information

species Oryza sativa
transcript LOC_Os05g26914.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G856084_T01 (Zea mays), 3'ss of exon 5
gtaagtactaaccattatat--gggaattgtgtttcagctac----ac--tcgatatattgcttctttttc--tcctttcgatccattataa-acctgagtactagttgttg--catta--cctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
|| |||  |  | |||  |   | ||||    ||||||||||    ||  ||   || ||| | |||||    | |||     |   | ||   ||||  || |  |  |||  |||||  | | | ||  |  ||   | ||||||||  ||    |||   | | |  | |  |||||||||||||||||||||||||||||||||||||| || ||||||||||||
gtgagt--tggctattgcaatagagaatcacttttcagctactatcaccatcatcattttgttgcttttcgggtgcttatagccagctgtactgcctgtatattcttctttgtacattagacatctctctcatttagtcagtcaaataatgaa--agtatctatttatgatctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G091811_T01 (Zea mays), 3'ss of exon 5
gtaagtactaaccattatatgggaattgtgtttcagctacactcgatatattgcttctttttctcctttcgatccattataaacctgagtactagttgttgcattacctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
                                                          |   |  || |  || | |  || |  ||  |  |     || ||   | | ||||  |  ||  || ||||||||  ||    ||    | | |  |||  ||||||||||||||||||||||||||||||||||| || |||||||||||||||
----------------------------------------------------------tagccagctgtacattcttcttatatttg--ttttgtacattaca---catatttcccatttagttagtcaaataatgaa--agtacctatttattgtttattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGAAATCAGCAATGCTTATGAG

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G14290.1 (Glycine max), 3'ss of exon 5
gtaagtactaaccattatatgggaattgtgtttcagctacactcgatatattgcttctttttctcctttcgatccattataaacctgagt--actagttgttgcattacctt---tttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
                                                                       | |  |   ||||   | |   |||||||    |||  ||    ||| || |||   | ||||  ||| | |||||  ||  | | | || |  |  ||||| ||||||||||||||||| || ||||| ||||||||||| ||||||
-------------------------------------------------------------------aataagctgtctcaaacacaattttgctagttgcataattttctggtattttatgacttgcttatcat-taaaccattgtc-tgtattt-tcttgtgttgcagAGAACCTGGTGCTGAACAAAAATTTAAGGAAATTAGCAATGCCTATGAG

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|58608089|gb|CK036122.1|CK036122
EST:     CCTATCGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|58673732|gb|CK062418.1|CK062418
EST:     GCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: GCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|58660788|gb|CK049468.1|CK049468
EST:     CCTATCGGAGGCTTGCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|58676612|gb|CK065299.1|CK065299
EST:     GAGTGCCTATCGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: GAGTGCCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
  tcataac  putative branch site (score: 2)
                                          tatttttcttt  putative PPT
         tacataatcaaataa  TA-rich tract