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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggcatactacctcgatacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatagatttcgtggtactgctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttgctattgacttatctttgcag

Basic information

species Oryza sativa
transcript LOC_Os11g36070.4
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g36070.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G104449_T03 (Zea mays), 5'ss of exon 9
AATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggc--atactacctcg-atacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatag-atttcgtggtact-gctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttgctattgacttatctttgcag
|||||||||||||||||| |||||||| || |||||||||||| | ||||||||||| |||||||||||||| |||||||| ||||| || ||||| ||||| ||||||   ||  |  | | | | ||  ||   | | || | || | |   ||||   ||||   |    ||| ||   |  |  | | |  ||  || |   | ||  |   |   |  ||||      || ||||| |        | || || ||||||   | || | ||||
AATAGCTAATATGGATATCAAGCTAGATTTTGTTCCACCATGGTTGATCAACTTCATGTCAAGGCAACTAATAGGCAGCGGGCATAAGCTGTATCAAAAGgttagtggctggtaacattttgcacatttcagttcagctgtgttctctaca---atagttttttttggaccatagtgtgtggtggaggtggtaaatcagggcatcagataaatactgcatgataattgatgagcatgagattc--------agcattt-ctattggaatgtcat-gcag

upper sequence: LOC_Os11g36070.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G135314_T01 (Zea mays), 5'ss of exon 2
AATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggcatactacctcgatacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatagatttcgtggtactgctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttg----ctattgacttatctttgcag
| ||||||||||||||||||||||||| || |||||||||||| | |||||||||||||||||||||||||| |||||||| ||||| || ||||| ||||| ||||||     |  |    || |||  | |   |||    |||||    |    ||| | |||| |  || ||||       || ||   |   | | | ||  | | |   ||  |||      || |||  |  ||  || |||||       ||| |||   || | |||||
AGTAGCTAATATGGATATTAAGCTAGATTTTGTTCCACCATGGTTGATCAACTTCATATCAAGGCAACTAATAGGCAGCGGGCATAAGCTGTATCAAAAGgttagtggctggtaatgttttcacatttcagctatattgtctacaata---gttttccttgtaccatagt-gtgtggtggggtggtaaatcagggcat-cagataaatcgtgcatgctgattaatgagcatgag--cttctaattgaacaccaataacctactgaagcatttctgcag

upper sequence: LOC_Os11g36070.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ31074 (Selaginella moellendorffii), 5'ss of exon 8
AATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggcatactacctcgatacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatagatttcgtggtactgctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttgctattgacttatctttgcag
  | |  ||||||||||| ||||| ||||| |||||||| ||| | |||||||||||  || |||| ||  ||||||| ||| | ||||| ||||| |||||      |    | |||  | |  |||||| |  | | |    |  |  ||  |   | ||||||                                                                                                            
GTTGGTCAATATGGATATAAAGCTCGACTTTGTTCCACCTTGGGTGATCAACTTCATCACACGGCAGCTCGTTGGCAGTGGCTACAAACTTTATCAAAAGgt-----acgcgttgcct--acaagtttgtgcttttctaa----accactcagcggtttgttcccag-----------------------------------------------------------------------------------------------------------

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|58606537|gb|CK034570.1|CK034570
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|88273561|gb|CI393967.1|CI393967
EST:     ACTTCATATCAAGGCAACTAATTTGCAGCGGCCATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|29688057|gb|CB684332.1|CB684332
EST:     ATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|27576960|gb|CA999654.1|CA999654
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTGTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|88581594|gb|CI698792.1|CI698792
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|27578183|gb|CB000878.1|CB000878
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTGTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|25778077|gb|CA752829.1|CA752829
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTGTATCAGAAG                         GCAGTCAGTAC
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTAC

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: 45 (upstream exon), 70 (downstream exon)
Score: 25

AATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGAGAACCACTCTATGTTAGAATCCGTGAGCACCGGGGTTCTACTGACATCG




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