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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaactgatgagtgcacgtgcaaaagatcatttgtgatgaaaggtcgtggttg...

Basic information

species Oryza sativa
transcript LOC_Os04g41100.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G179097_T01 (Zea mays), 5'ss of exon 9
TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaa-ctgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
                                 ||||| ||||||||||||||||||||||| || |||||||||||||| || |||||||||||  ||||||| | |||  |||| ||| || |  |||||||||| ||||| ||||||| ||  ||||||   | |          ||||||||  ||  | |||| | | |     
---------------------------------AAGCGCAGGGGAAGGATGCCTTTTGCTTT-CATCAGGAAATCAATGG-CATTAATACAACTTAGAAGgtaa-tgtatg-aaaagccaattgctgcaagtgatgtgttgctaactaaaaactagtgagtgtgggagttcttcactgaaagatcagctgc-acgaaatg-cat-----

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G179097_T02 (Zea mays), 5'ss of exon 8
TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaa-ctgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
   ||||| | ||||||||||||||||||| ||||||| ||||||||||||||||||||||| || |||||||||||||| || |||||||||||  ||||||| | |||  |||| ||| || |  |||||||||| ||||| ||||||| ||  ||||||   | |          ||||||||  ||  | |||| | | || |  
---TCTTTGCGTTTTGTTTGCAAGAGACAAAAGAAGCGCAGGGGAAGGATGCCTTTTGCTTT-CATCAGGAAATCAATGG-CATTAATACAACTTAGAAGGTAA-Tgtatg-aaaagccaattgctgcaagtgatgtgttgctaactaaaaactagtgagtgtgggagttcttcactgaaagatcagctgc-acgaaatg-catgatat

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G179097_T03 (Zea mays), 5'ss of exon 7
--TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaa-ctgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
  |||||||| | ||||||||||||||||||| ||||||| ||||||||||||||||||||||| || |||||||||||||| || |||||||||||  ||||||| | |||  |||| ||| || |  |||||||||| ||||| ||||||| ||  ||||||   | |          ||||||||  ||  | |||| | | |     
TTTGATCTTTGCGTTTTGTTTGCAAGAGACAAAAGAAGCGCAGGGGAAGGATGCCTTTTGCTTT-CATCAGGAAATCAATGG-CATTAATACAACTTAGAAGgtaa-tgtatg-aaaagccaattgctgcaagtgatgtgttgctaactaaaaactagtgagtgtgggagttcttcactgaaagatcagctgc-acgaaatg-cat-----

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 8
--TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgacta-aaactgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
  |||||||| ||||||||||||||||||| | ||||||| |||||||||| ||||||||||||| | ||||||||||||| ||| |||||||||||  ||||||| ||||| ||||| ||| || |  ||||||| || ||||| |||| ||||| ||||  |   | |          ||| ||||  ||     || ||         
TTTGATCTTTGCATTTTGTTTGCAAGAGACGAAAGAAGCGCAGGGGAAGGAAGCCTTTTGCTTTT-ATCAGGAAATCAATG-ACATTAATACAACTTAGAAGgtaa-tatat-caaaagccaattgctgcaagtgacgtgttgctaactagaaactaatgaacgagggagttctttactgaaaaatcaggtgcatgaaatggat-------

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|87021463|gb|CI274070.1|CI274070
EST:     GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
EST: gi|88291287|gb|CI529877.1|CI529877
EST:     TTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTTAAGCTNTGGCTGGTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: TTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
EST: gi|29628989|gb|CB634000.1|CB634000
EST:     GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
EST: gi|27920887|gb|CB096695.1|CB096695
EST:     GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
EST: gi|218495458|gb|FG950145.1|FG950145
EST:     GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
EST: gi|88286911|gb|CI520221.1|CI520221
EST:     GGACAGTAATACAACTTGAAAG                         CTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: GGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT

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: 59 (upstream exon), 73 (downstream exon)
Score: 7

TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTTGTACCTAAGTGACTAAATTTTGTGGAAGGTCTTCAAGAGAGTTCACCTG




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