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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtagtatttggctaattaaatgcttaaagctttcatctagaccaatttgacacctctatatacacatctataatgtgttgttggtttctcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATACTGTGATACGCCGCCTGCCTGATGATGATGTACAATGTCTCGCTCTAGGA

Basic information

species Oryza sativa
transcript LOC_Os02g51500.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51500.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G012269_T01 (Zea mays), 3'ss of exon 2
--tggt-agtatttggctaatta-aatgcttaaagctttcatctagaccaatttgacacctctatatacacatctataatgtgttgttggtttctc-ctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATACTGTGATACGCCGCCTGCCTGATGATGATGTACAATGTCTCGCTCTAGGA-
  || | | |||     ||| |   ||||| |||||| |  |   ||     ||||||  | | || ||| | || |||  |||||||    | |   |||||||||||||||||||||||||||  ||||||||||||||| ||||| ||||| || ||||| | ||||||| ||||| || |  |   ||| | |   ||||| 
gttgtttaatatgatcttaactgtgatgctgaaagctattgt---gattttcttgaca--tttgtaaacatacctctaacatgttgttcacctataattttccagAGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTCTCTGATAAGACGCCTGCTTGATGTTG-TACAATCTGTGTAGTCTTAGGAT

upper sequence: LOC_Os02g51500.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G025470_T01 (Zea mays), 3'ss of exon 2
tggtagtatttggctaattaaatgcttaaagctttcatcta----gaccaatttgacacctctatatacacatctataatgtgttgttggtttctcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATACTGTGATACGCCGCCTGCCTGATGATG-ATGTACAATGTCTCGCTCTAGGA
   || |  |||  ||||   |||  | | ||    | |||    ||     ||   ||   | |  ||| |  | |||  ||||      |   | || ||||||||||||||||| |||||||||||||||||||||||||| || ||||| || ||||| | || |||| || || || |    |  ||| |     || | 
--ctattcattgattaatatgatgactgatgccaaaagctattatgattttcttatgacacttgtgaacatacttctaacatgtt--cacctgtactttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTCTCTGATAAGGCGTCTGCTTGGTGCTGTACAATCTGTGTGTACACATAAG-
















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|58604515|gb|CK015043.1|CK015043
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAAGCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCCC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCC
EST: gi|29670191|gb|CB666466.1|CB666466
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|38475588|gb|CF959721.1|CF959721
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCC
EST: gi|88240110|gb|CI239272.1|CI239272
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88732429|gb|CI755606.1|CI755606
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGAT
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGAT
EST: gi|25799893|gb|CA755854.1|CA755854
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88436056|gb|CI516592.1|CI516592
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|33681776|gb|CF310015.1|CF310015
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88289982|gb|CI547619.1|CI547619
EST:     CATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: CATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|33684024|gb|CF312263.1|CF312263
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGGTGTACCATA
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGG-TGTACCATA
EST: gi|218499796|gb|FG963827.1|FG963827
EST:     AATTACGATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGA
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGA
EST: gi|33683196|gb|CF311435.1|CF311435
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGNTGGGTGTACCATA
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATG-TGGGTGTACCATA
EST: gi|88478522|gb|CI415793.1|CI415793
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88471386|gb|CI408657.1|CI408657
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88511850|gb|CI439356.1|CI439356
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88481575|gb|CI418846.1|CI418846
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88963349|gb|CI028365.1|CI028365
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|86853635|gb|CI330486.1|CI330486
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgacacctctatatacacatctataatgtgttgttggtttctcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATACTGTGATACGCCGCCTGCCTGATGATGATGTACAATGTCTCGCTCTAGGA
 atttgac  putative branch site (score: 4)
                                     ttggtttctcctttcc  putative PPT
                      atctataat  TA-rich tract