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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgaggcagctaagtcgaatttacaatatcaaaatgggctagcaaaacatggcctaaggcttttgtttacaacacaacatcgttgaaaattaatagtactctaggctttcaccctttgctgactgtatttgtctgctatactgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g53110.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G159295_T02 (Zea mays), 3'ss of exon 7
gtaagttgaggcagctaagtcgaa--tttacaatatcaaaatgggctagcaaaacatggcctaaggcttttgtttacaacacaacatcgttgaaaattaatagt---------actctaggctttcaccctttgctgac--tgtatttgtctgctatactgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
||||||||   ||||| | |  ||  ||||||  |||| |||   |||||||| | || ||| | | |  |||| |||     |  |  || ||   ||||  |         | | |||| |||  | || || ||||  ||||||||| ||  | ||  |||||| ||||||||||||| |||||||| ||||||||||| |||||||||
gtaagttggcacagctgattttaagttttacagcatcacaataaactagcaaagcctgcccttatgttgctgttcacatgggtatttt-ttaaattctaatgttgtaagagaaattttagggtttagctctgtgttgacgttgtatttgtttgtgacaccttttcagTTGAGAGAGTACATCGATGACACGGAAGATTACATCAATATCCAG

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 7
gtaagttgaggcagctaagtcgaatttacaatatcaaaatgggctagcaaaacatggcctaaggcttttgtttacaacacaacatc---gttgaaaattaatagtactctaggctttcaccctttgctgactgtatttgtctgctatactgtttca-gCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG---------------------------------------
                                                          ||  |   |||  ||| |       |       |   ||||     ||||  |   ||| ||  ||  || | |   ||| | |    |    ||| | |||| |||||||||||||||| || |||||||| |||||||| ||                                        
----------------------------------------------------------ctgtgttatttacttagataggtttacttgaactctgaatttgctatactagatagttttacttttacctaattacttttctttttcttttcatttaaagCTGCGAGAGTACATTGATGATACTGAAGATTATATTAATATTCAAGTAAGTAGCTAGCAATTTACTGATAATATATCAATTGGT

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 7
gtaagttgaggcagctaagtcgaatttacaatatcaaaatgggctagcaaaacatggcctaaggcttttgtttacaacacaacatcg-ttgaaaattaatagtactctaggctttcaccctttgctgactgtatttgtctgctatactgtttca-gCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
                                                        ||||     ||   | | ||     || |    |   ||||    |||||  |   ||| ||  ||  || | |   ||| | |    |    ||| | |||| |||||||||||||||| || |||||||| |||||||| || 
--------------------------------------------------------gcctgttatttacatattcaggtttacctgaactctgaatttgctgtactagatagttttacttttacctaattacttttctttttcctttcatttaaagCTGCGAGAGTACATTGATGATACCGAAGATTATATTAATATTCAA

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G35260.1 (Glycine max), 3'ss of exon 7
gtaagttgaggcagctaagtcgaatttacaatatcaaaatgggctagcaaaacatggcctaaggcttttgtttacaacacaacatc---gttgaaaattaatagtactctaggctttcaccctttgctgactgtatttgtctgctatactgtttca-gCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
                                                          ||  |   |||  ||| |       |       |   ||||     ||||  |   ||| ||  ||  || | |   ||| | |    |    ||| | |||| |||||||||||||||| || |||||||| |||||||| || 
----------------------------------------------------------ctgtgttatttacttagataggtttacttgaactctgaatttgctatactagatagttttacttttacctaattacttttctttttcttttcatttaaagCTGCGAGAGTACATTGATGATACTGAAGATTATATTAATATTCAA

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagttgaggcagctaagtcgaatttacaatatcaaaatgggctagcaaaacatggcctaaggcttttgtttacaacacaacatcgttgaaaattaatagtactctaggctttcaccctttgctgactgtatttgtctgctatactgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
                                                                           |    | | || |||    |   | ||  |   ||  |   |   ||    | | || |||      |   || | |||||  | ||||| |||||||||||||| ||||||||||| ||||||
-------------------------------------------------------------------------gtattgtatcttc-ttgttcctgtttcgtctttgtggtatctccgacttagaaagtataattg------aacatgatgcagCTACGCGAGTATATTGATGACACAGAGGATTACATTAACATCCAG

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G09690.4 (Arabidopsis thaliana), 3'ss of exon 6
------------------------gtaagttgaggcagcta--agtcgaatttacaatatcaaaatgggctagcaaaacatggcctaaggcttttgtttacaacacaacatcgttgaaaattaatagtact--ctaggctttcaccctttgctgactgtatttgtctg-ctatac-tgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
                          ||||  |  || | |  | |   ||||    ||  |        |     || || | | |   ||||     |    ||       ||| |  ||  |  | ||   | | ||||      |  | ||||      || |   |  || || | |||||  | ||||| |||||||||||||| ||||||||||| ||||||
gtaatacttgtttccagctacatatgaagtataaacaaccattaatgtgatttttgttaataggcatacttcatgcaa-atagac-agcactttgaacaaattaaccgaggtattgtatcttcttgttcctgtttcgtctttgtggtatctccgacttagaaagtataattgaacatgatgcagCTACGCGAGTATATTGATGACACAGAGGATTACATTAACATCCAG

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|86491085|gb|CI133718.1|CI133718
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|3763402|gb|AU030154.1|AU030154
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|88845073|gb|CI083998.1|CI083998
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|38468461|gb|CF952592.1|CF952592
EST:     TGGAGGCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: TGGAGGCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|89181743|gb|CI113249.1|CI113249
EST:     GCATAGTTCATGCAAATTGATGGCACATTAAACAAATTGACGACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|86495286|gb|CI137919.1|CI137919
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|86496775|gb|CI139408.1|CI139408
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|27547079|gb|CA767318.2|CA767318
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|88840990|gb|CI000952.1|CI000952
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATCGACAACG                         CTGAGAGAGTACATTGATGA-ACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|88476382|gb|CI413653.1|CI413653
EST:     AAACAGATTGACNACG                         NTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: AAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|2797458|gb|AA750752.1|AA750752
EST:     GCATACTTCATGCAAATTGGATGGCACATTAAACAAATTGCCAACG                         CTGAGAGAGTACATTGATGACACA
genomic: GCATACTTCATGCAAATTG-ATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACA
EST: gi|89178025|gb|CI391204.1|CI391204
EST:     TGGAGGCATACTTCAGGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: TGGAGGCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|86252029|gb|CI055766.1|CI055766
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|58674510|gb|CK063197.1|CK063197
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|88963590|gb|CI029384.1|CI029384
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
EST: gi|58683065|gb|CK071752.1|CK071752
EST:     GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACG                         CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
genomic: GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 70 (upstream exon), 69 (downstream exon)
Score: 18

GCATACTTCATGCAAATTGATGGCACATTAAACAAATTGACAACGgtaagttgag ... actgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtactctaggctttcaccctttgctgactgtatttgtctgctatactgtttcagCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG
                      tgctgac  putative branch site (score: 18)
                                              ctgtttc  putative PPT
                             tgtattt  TA-rich tract