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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtggccttctcatgtctcgatcggatcgtgtgatgataattcgtactcacaccgtctgcaattttgtgggtggaagcagcagcattgcttgctcgggctcctgaataatgggagcggttactttcgttgcgcatatttggatgttaatgacggatttgtggtgtcgtgatgcagGTATCTGGCGACGCCTTGGCTCGCCAGCCCACATTTGCAGACACTGTTCCTGGGTATCTCCGGGAGGCCACCTTCGTTCACATACAAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g65070.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G005444_T01 (Zea mays), 3'ss of exon 1
gtttgtgtggccttctcatgtctcgatcggatcgt-gtgatg-ataattcgtactcacaccgtctgcaatt--ttgtgggtggaagcagcagcattgct-tgctcgggctcctgaataatgggagcggttactttcgttgcgc-----atatttgga--tgttaatgac--ggatttgtggtgtcg-tgatgcagGTATCTGGCGACGCCTTGGCTCGCCAGCCCACATTTGCAGACACTGTTCCTGGGTATCTCCGGGAGGCCACCTTCGTTCACATACAAAAG
    || ||||  |      ||| |  |||||||| ||  || |    | ||||   ||  |   |   ||  |     |||   | |   ||| || | || |  | || |||||  | | ||  | ||| || |  || |      ||| ||  |  ||    |||   ||||||||||| |   | |||||||||||||||||| || ||||| || ||||| |||||||||||| |||||||||| || | ||||| ||| ||||| ||||||||||| ||
----gtatggctatgggccctctaggccggatcgtcgtagtgtagcggtagtaccagcattgggcgtgtttggtcaactgtgatggaatttgcaatgttgtgttttgacttctgaaacacgcgatggattatttccactgtgtgatgaatagtttaagctgggggtgatatggatttgtggtattaattatgcagGTATCTGGCGACACCATGGCTGGCGAGCCCGCATTTGCAGACATTGTTCCTGGGCATTTACGGGACGCCGCCTTCATTCACATACAAGAG
















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|58668684|gb|CK057370.1|CK057370
EST:     CCGAGATCTACCACCGCTGTA-CCTCCAAGTGCCGCTCCCTCCACGGCAG                         GTATCTGGCGACGCCTTGTGCTCGCCAGCCCACATTTGCAGACACTGTTCC
genomic: CCGAGATCTACCACCGC-GTAGCCTCCAAGTGCCGCTCCCTCCACGGCAGgtttgtgtgg ... cgtgatgcagGTATCTGGCGACGCCTTG-GCTCGCCAGCCCACATTTGCAGACACTGTTCC
EST: gi|66921886|gb|CX108734.1|CX108734
EST:     TCCGAGATCTACCACCGCGTAGCCTCCAAGTGCCGCTCCCTCCACGGCAG                         GTATCTGGCGACGCCTTGGCTCGCCAGCCCACATTTGCAGACACTGTTCCT
genomic: TCCGAGATCTACCACCGCGTAGCCTCCAAGTGCCGCTCCCTCCACGGCAGgtttgtgtgg ... cgtgatgcagGTATCTGGCGACGCCTTGGCTCGCCAGCCCACATTTGCAGACACTGTTCCT
EST: gi|28298246|gb|CB238476.1|CB238476
EST:     TCCGAGATCTACCACCGCGTAGCCTCCAAGTGCCGCCCCCTCCACGGCAG                         GTATCTGGCGACGCCTTGGCTCGCCAGCCCACATTTGCAGACACTGTTCCT
genomic: TCCGAGATCTACCACCGCGTAGCCTCCAAGTGCCGCTCCCTCCACGGCAGgtttgtgtgg ... cgtgatgcagGTATCTGGCGACGCCTTGGCTCGCCAGCCCACATTTGCAGACACTGTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttcgttgcgcatatttggatgttaatgacggatttgtggtgtcgtgatgcagGTATCTGGCGACGCCTTGGCTCGCCAGCCCACATTTGCAGACACTGTTCCTGGGTATCTCCGGGAGGCCACCTTCGTTCACATACAAAAG
                      tgttaat  putative branch site (score: 3)
                     atgttaat  TA-rich tract