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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattggaattcgttgtttgacatattactttaatttatgtatttagtaactgtttttattgaatgtagctcacagttccaagctgttttgattctgtaatgttctattgttctttaatggatctttgttgctcgccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGACGAGCATCACCACTAAGGACGCCCATGCCTCGTGGTTCTGATAATAAGAA

Basic information

species Oryza sativa
transcript LOC_Os01g42650.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G477366_T01 (Zea mays), 3'ss of exon 4
gtaattggaattcgttgtttgacatattactttaatttatgtatttagtaactgtttttattgaatgtagctcacagttccaagctgttttgattctgtaatgtt-ctattgttctttaatggatcttt---gttgctcgccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGACGAGCATCACCACTAAGGACGCCCATGCCTCGTGGTTCTGATAATAAGAA------
                                ||||||| ||   ||  |||||||| |  ||  | ||  | |  | | ||  |  |     | |  |  || | |   ||||  |||||| |  | |   |||||| |  || |||||||||||||||||||||||||||||||||||||||| ||||  ||||| || ||    || |||||||||      ||||| |||||||||| ||||||||      
-------------------------------gtaatttaagtcccta--aactgtttgttatgc-tataagttattgctaca--caatcacactgccatgctgatgccggtgttaattaatgtaattatttggttgcttgatttgtgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGTCATGGCGATGAAGATGATGGACATCACTAAGGA------TGCCTTGTGGTTCTGAAAATAAGAACTTGGT

upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G134738_T02 (Zea mays), 3'ss of exon 5
gtaattggaattcgttgtttgacatattactttaatttatgtatttagtaactgtttttattgaatgtagctcacagttcca-agctgttttgattctgtaatgttctattgttctttaatggatcttt---gttgctcgccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGACGAGCATCACCACTAAGGACGCCCATGCCTCGTGGTTCTGATAATAAGAA------
                        |  || | ||| |    |  | | |  ||||||  ||  | ||||| | |  | | || |    |  ||  |   | ||||     | ||   ||||| |  | |   |||||| |  || ||||||||||||| |||||||||||||| ||||||||||| ||||| ||||| || ||    || |||||||||      ||||| |||||||||| ||||||||      
-----------------------gtggtaatctaaat----tgctaaattgctgtttg-atatactgtaggttattgctacacaagcatactgcatgc-tgatgtc--ggtattaactaatgtaattatttggttgcttgatttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGA------TGCCTTGTGGTTCTGAAAATAAGAATCTGAT

upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AC234517.1_FGT001 (Zea mays), 3'ss of exon 4
gtaattggaattcgttgtttgacatattactttaatttatgtatttagtaactgtttttattgaatgtagctcacagttccaagctgttttgattctgtaatgtt-ctattgttctttaatggatcttt---gttgctcgccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGACGAGCATCACCACTAAGGACGCCCATGCCTCGTGGTTCTGATAATAAGAA
                                ||||||| ||   ||  |||||||| |  ||  | ||  | |  | | ||  |  |     | |  |  || | |   ||||  |||||| |  | |   |||||| |  || |||||||||||||||||||||||||||||||||||||||| ||||  ||||| || ||    || ||||||                                  
-------------------------------gtaatttaagtcccta--aactgtttgttatgc-tataagttattgctaca--caatcacactgccatgctgatgccggtgttaattaatgtaattatttggttgcttgatttgtgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGTCATGGCGATGAAGATGATGGACATCACTAA----------------------------------

upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G134738_T01 (Zea mays), 3'ss of exon 5
gtaattggaattcgttgtttgacatattactttaatttatgt-atttagtaactgtttttattgaatgtagctcacagttcca-agctgttttgattctgtaatgttctattgttctttaatggatcttt---gttgctcgccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGACGAGCATCACCACTAAGGACGCCCATGCCTCGTGGTTCTGATAATAAGAA------
                                |||| ||  |   | | |  ||||||  ||  | ||||| | |  | | || |    |  ||  |   | ||||     | ||   ||||| |  | |   |||||| |  || ||||||||||||| |||||||||||||| ||||||||||| ||||| ||||| || ||    || |||||||||      ||||| |||||||||| ||||||||      
-------------------------------gtaatctaaattgctaaattgctgtttg-atatactgtaggttattgctacacaagcatactgcatgc-tgatgtc--ggtattaactaatgtaattatttggttgcttgatttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGA------TGCCTTGTGGTTCTGAAAATAAGAATCTGAT

upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AC215864.3_FGT010 (Zea mays), 3'ss of exon 3
gtaattggaattcgttgtttgacatattactttaatttatgtatttagtaactgtttttattgaatgtagctcacagttccaagctgttttgattctgtaatgtt-ctattgttctttaatggatcttt---gttgctcgccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGACGAGCATCACCACTAAGGACGCCCATGCCTCGTGGTTCTGATAATAAGAA
                                ||||||| ||   ||  |||||||| |  ||  | ||  | |  |  | | ||  |     | |  |  || | |   ||||  |||||| |  | |   |||||| |  || ||||||||||||||||||||||||||||||||| |||||  ||||| ||||| || ||    || ||||||                                  
-------------------------------gtaatttaagtcccta--aactgtttgttatgc-tataagttattg--ctacgcaatcacactaccatgctgatgccggtgttaattaatgtaattgtttggttgcttgatttgtgcagCTTAAGGTCATTGGTGATGGTGGTGATCTAGATGTTCATGACGATGAAGATGATGGACATCACTAA----------------------------------

upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G064753_T01 (Zea mays), 3'ss of exon 5
gtaattggaattcgttgtttgacatattactttaatttatgtatttagtaactgtttttattgaatgtagctcacagttcca-agctgttttgattctgtaatgttc-tattgttctttaatggatctttgttgctcgccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGACGAGCATCACCACTAAGGACGCCCATGCCTCGTGGTTCTGATAATAAGAA------
                                ||||||| ||   ||  |||||||| |  ||  | ||  | |  | | || |   |   ||      | ||| |  | ||  |  ||        || |||||| |  || |||||||||||||||||||||||||||||||||||||||| ||||| ||||| || ||    || |||||||||      ||||| |||||||||| ||||||||      
-------------------------------gtaatttaagtcccta--aactgtttgttatgc-tataagttattgctacacaatcgcactgccatgctgatgctggtgttaattattgtaattatttggttgcttgatttgtgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGTCATGACGATGAAGATGATGGACATCACTAAGGA------TGCCTTGTGGTTCTGAAAATAAGAATTTGGT

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|88518836|gb|CI445682.1|CI445682
EST:     -ANAAAAAGATGAACCGCATGAGTNCCCAGTCTGTTCACAATATTTTGTG                         CTTAAGGTCATTGGTGATGNTGGTGATCCAGATGGACATGATGATGACGAC
genomic: GA-AAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTGgtaattggaa ... ccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
EST: gi|33797913|gb|CF324816.1|CF324816
EST:     TGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG                         CTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
genomic: TGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTGgtaattggaa ... ccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
EST: gi|29646177|gb|CB651184.1|CB651184
EST:     TGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG                         CTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
genomic: TGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTGgtaattggaa ... ccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
EST: gi|163917851|gb|EG714745.1|EG714745
EST:     GAGTGCCCAGTCTGTTCACAATATTTTGTG                         CTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
genomic: GAGTGCCCAGTCTGTTCACAATATTTTGTGgtaattggaa ... ccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
EST: gi|88226660|gb|CI226576.1|CI226576
EST:     CAGTCTGTTCACAATATTTTGTG                         CTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
genomic: CAGTCTGTTCACAATATTTTGTGgtaattggaa ... ccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
EST: gi|5771168|gb|AU078014.1|AU078014
EST:     ATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG                         CTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
genomic: ATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTGgtaattggaa ... ccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
EST: gi|8335467|gb|BE040401.1|BE040401
EST:     TGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG                         CTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
genomic: TGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTGgtaattggaa ... ccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
EST: gi|5005118|gb|AU069902.1|AU069902
EST:     TGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG                         CTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC
genomic: TGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTGgtaattggaa ... ccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGAC

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: 74 (upstream exon), 74 (downstream exon)
Score: 141

AGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTGgtaattggaa ... ccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGACGAGCATCACCACTAAGGACGCCCATGCCTCGTGGTTCTGATAATAAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattctgtaatgttctattgttctttaatggatctttgttgctcgccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGACGAGCATCACCACTAAGGACGCCCATGCCTCGTGGTTCTGATAATAAGAA
                      ctttaat  putative branch site (score: 141)
                                         ctcgcctttt  putative PPT
               tattgttctttaat  TA-rich tract