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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttcctgatcgattgcgcctccctccccctcctcgtcgcgctctcccgctgcgcatctcaccatttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT

Basic information

species Oryza sativa
transcript LOC_Os05g41110.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044137_T02 (Zea mays), 3'ss of exon 1
gtaaggttcctgatcgattgcgcctccctccccctcc-tcgtcgcgctctcccgctgcgcatctcaccatttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT---
               |  ||  || |   |  ||||  | |   | |||| || || ||      |   |||   || ||||||  |  |||| ||   ||    ||||  |      ||||||||||||||||| || | ||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||   
---------------gtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtgaa---ttttcctgtgatgttgat--tggtctcccgtt----ggtttcgat--ctatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044137_T01 (Zea mays), 3'ss of exon 1
gtaaggttcctgatcgattgcgcctccctccccctcc-tcgtcgcgctctcccgctgcgcatctcaccatttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT
               |  ||  || |   |  ||||  | |   | |||| || || ||      |   |||   || ||||||  |  |||| ||   ||    ||||  |      ||||||||||||||||| || | ||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||
---------------gtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtgaa---ttttcctgtgatgttgat--tggtctcccgtt----ggtttcgat--ctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv13s0064g00850.t01 (Vitis vinifera), 3'ss of exon 1
gtaaggttcctgatcgattgcgcctccctccccctcctcgtcgcgctctcccgctgcgcatctcaccatttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgat-gcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT
       | | ||     |   | |   |||||   ||  |     ||  |  ||   |   |||  |    | ||  |||  |||  |  | | |||||  || |||||   |   ||  ||||||||||     || |||||||||||||||||    || ||||||||||||||||||||||||||||||||||||||||| |||||||  ||  | | ||
------gtacggacatcgtattcgttgttccccgatcttatt---ttcaacttctctacgattcaaga----gatgtaatgcatttcattttgtttgattt-tgtgttgttttggaaatcacagAAGAAGACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCT

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1
----gtaaggttcctg-atcgattgcgcctccctccccctcctcgtcg------cgctctc-ccgctgcgcatct--caccatttcgttgcgatgtttttgctggtttctga--ttggtgggttgtg------gcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT
    ||| ||    || |         |   || |  ||  |    ||      |||   |  |||||  | ||   |   |  | | | | |  |     | ||| |   |  | ||| |   | |      | |     ||||||||||| |  ||| |||||||||  |   |||  ||||||||||||||| ||||||||||| || ||||||||||||  ||| ||||| ||||||    
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcgctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG

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|88400326|gb|CI591016.1|CI591016
EST:     GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT
                        ttctgat  putative branch site (score: 3)
          atgttttt  TA-rich tract