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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagatcattttccactgatgcaaaactctggttttgttattggttaactgccatcttaatattagtccttttttattttttggatgcagAGGCAATTATATGAAGCTTTTCTTAACAGTGAACTAGTTCATTCATCAATGCAAGGGTCACCCTTGGCCGCAATCACG

Basic information

species Oryza sativa
transcript LOC_Os04g59624.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59624.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G138125_T02 (Zea mays), 3'ss of exon 8
gtacagatcattttccactgatgcaaaactctggttttgttattggttaactgccatcttaatattagtccttttttattttttggatgcagAGGCAATTATATGAAGCTTTTCTTAACAGTGAACTAGTTCATTCATCAATGCAA------GGGTCACCCTTGGCCGCAATCACG
||    ||    |  ||  | |   |||   || ||  | ||||| ||||     || ||  |  | ||    ||    | | || ||||||||| || |||||||||||||||| || ||||| || ||||||| | || ||||       |  ||||| ||||| |||||||| 
gtttgaatttggtgtcatcgttatgaaaagttgtttgagctattgattaatgattatttt--ttctggtgacctt----tctatgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTGCAGCCAAAGGCATCACCGTTGGCTGCAATCACA

upper sequence: LOC_Os04g59624.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G63950.1 (Arabidopsis thaliana), 3'ss of exon 10
gtacagatcattttccactgatgcaaaactctggttttgttattggttaactgccatcttaatattagtccttttttattttttggatgcagAGGCAATTATATGAAGCTTTTCTTAACAGTGAACTAGTTCATTCATCAATGCAAGGGTCACCCTTGGCCGCAATCACG
|| || | | ||   ||   |   | |    | | |    ||||   ||| |    |   | || |  | |||    || | || | |||||||||||||||||||||||||  | ||||||||| | ||||  ||| |  |  | || |||||  | || ||  | |||
gtgca-acccttaaacatacaactacagtcgttgatcaaatatt--ctaagtcttttggaattactgatactt----atctctttgttgcagAGGCAATTATATGAAGCTTTCTTAAACAGTGAAATTGTTCTGTCAGCTTTTGATGGTTCACCTCTAGCAGCTCTAACG
















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|33678103|gb|CF306342.1|CF306342
EST:     TTGCTAAGAAGAATGAGCTAATTATCTGGCTGAAATTAACATCTTGCCAG                         AGGCAATTATATGNAAGCTTTTCTTAACAGTGAACTAGTTCATTCATCAAT
genomic: TTGCTAAGAAGAATGAGCTAATTATCTGGCTGAAATTAACATCTTGCCAGgtacagatca ... ttggatgcagAGGCAATTATATG-AAGCTTTTCTTAACAGTGAACTAGTTCATTCATCAAT
EST: gi|58680097|gb|CK068784.1|CK068784
EST:     TTGCTAAGAAGAATGAGCTAATTATCTGGCTGAAATTAACATCTTGCCAG                         AGGCAATTATATGAAGCTTTTCTTAACAGTGAACTAGTTCATTCATCAATG
genomic: TTGCTAAGAAGAATGAGCTAATTATCTGGCTGAAATTAACATCTTGCCAGgtacagatca ... ttggatgcagAGGCAATTATATGAAGCTTTTCTTAACAGTGAACTAGTTCATTCATCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttattggttaactgccatcttaatattagtccttttttattttttggatgcagAGGCAATTATATGAAGCTTTTCTTAACAGTGAACTAGTTCATTCATCAATGCAAGGGTCACCCTTGGCCGCAATCACG
                   tcttaat  putative branch site (score: 3)
                               tccttttttatttttt  putative PPT
                  atcttaatattagtcc  TA-rich tract