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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtatttatgtggttatgttcaagataagttactgtgcatactaattctagatagataaaatattttgatgaaaattagatcatagcatgacttatgttgtgcttccattgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG

Basic information

species Oryza sativa
transcript LOC_Os01g58690.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g58690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G086246_T01 (Zea mays), 3'ss of exon 3
-----------------------------gtatggtatttatg-tggttat---gttcaagataagttactgtgca-tactaattctagata-gataaaatattttgatgaaaattagat-catagcatgacttatgttgtgcttccat-tgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG
| | ||| | || || || | || | |||| || |||| | ||| || ||||| | | || || || | | |||| ||| ||| | ||| || |||||| ||||||| || || ||||| ||| ||||||||| || |||||||| || |||||| ||||||| |||||||||||| ||||||||||
gtatgttcttcctgtggttaatgcccaacatctcccttttgtactgactaaaaagtcagtggatagcagcattgcaataaatcttctgaacccaatactatcagttgatacatagtatatatctaacctcactttccgtgttcttttgtatgcattaacagGTACAACCAATCTCAGTTCAATATGGGCTTGGCATACCAGAGCATGATCAGGAAGGCAGGCTTATTACCTTGGAGTTTGATGATTTTTACTTG-------

upper sequence: LOC_Os01g58690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G800154_T01 (Zea mays), 3'ss of exon 5
-----------------------------gtatggtatttatg-tggttatgttcaagataagttactgtgc-atactaattct----agatagataaaatattttgatgaaaattagat-catagcatgacttatgttgtgcttccat-tgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG
| | ||| | || || | | | | | | ||| ||| | ||| || ||||| | | || || || | | |||| ||| ||| | ||| || |||||| ||||||| || || ||||| ||| ||||||||| || | |||||| || |||| | ||||||| |||||||||||| |||||||||||| ||||
gtatgttctttctatggttaatgcccaacatctcccttttgtactgactaaaaactcagtggatagcagcattgcaataaatcttctgaacccaatactatcagttgatacatagtatatatctaacctcactttctgtgttcttttgtatgcattaacagGTACAACCAATCTCAGTTCAATATGGGCTTGGCATACCAGAGCGTGATCAGGAAGGCATGCTTATTACCTTGGAGTTTGATGATTTTTACTTGGTCAATG

upper sequence: LOC_Os01g58690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G139329_T02 (Zea mays), 3'ss of exon 3
---------------------------gtatggtatttatgtggttatgttcaagataagttactgt-gcatactaat------tctagata-gataaaatattttgatgaaaattagat-catagcatgacttatgttgtgcttccat-tgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG
| || || ||| | | ||| | | | |||| ||| ||| | ||| || ||||| | | || || || | | |||| ||| ||| | ||| || |||||| ||||||| || || ||||| ||| ||||||||| || |||||||| || |||||| ||||||| |||||||||||| |||||||||||| ||||
gtatgttcttcctgtggttaatgcccagcatctcccttttgtactgactaaaaagtcagtggatagcagcattgcaataaatcttctgaacccaatactatcagttgatacatagtatatatctaacctcactttccgtgttcttttgtatgcattaacagGTACAACCAATCTCAGTTCAATATGGGCTTGGCATACCAGAGCATGATCAGGAAGGCAGGCTTATTACCTTGGAGTTTGATGATTTTTACTTGGTCAATG

upper sequence: LOC_Os01g58690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G134072_T02 (Zea mays), 3'ss of exon 4
-----------------------------gtatggtatttatg-tggttat---gttcaagataagttactgtgca-tactaattctagata-gataaaatattttgatgaaaattagat-catagcatgacttatgttgtgcttccat-tgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG
| | ||| | || || || | | || | |||| || |||| | ||| || ||||| | | || || || | | |||| ||| ||| | ||| || |||||| ||||||| || || ||||| ||| ||| |||| || | |||||| || |||||| ||||||| |||||||||||| |||||||||||| ||||
gtatgttcttcttatggttaatgcccaacatctcccttttgtactgactaaaaagtcaatggatagcagcattgcaataaatcttctgaacccaatactatcagttgatacatagtatatatctaacctcactttccgtgttcttttgtatgcattaacagGTACAACCAATCTCAGTTCAATATGGGCTTGACATAACAGAGCGTGATCAGGAAGGCAGGCTTATTACCTTGGAGTTTGATGATTTTTACTTGGTCAATG

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|27546396|gb|CA764589.2|CA764589
EST:     CATGCAGCGTCTCGAGGCTTGGCTATTCAGGGACTGCTGTAATTTCACGG                         GTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCAT
genomic: CATGCAGCGTCTCGAGGCTTGGCTATTCAGGGACTGCAGTAATTTCACGGgtatggtatt ... gcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCAT
EST: gi|66927262|gb|CX114110.1|CX114110
EST:     CATGCAGCGTCTCGAGGCTTGGCTATTCAGGGACTGCAGTAATTTCACGG                         GTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCAT
genomic: CATGCAGCGTCTCGAGGCTTGGCTATTCAGGGACTGCAGTAATTTCACGGgtatggtatt ... gcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCAT

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: 28 (upstream exon), 54 (downstream exon)
Score: 4

GGATGTTGAAAAGTTTAAGAATCTGATAGCAGACTATGACAGCTATTGGTCATGCAGCGTCTCGAGGCTTGGCTATTCAGGGACTGCAGTAATTTCACGGgtatggtatt ... gcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgaaaattagatcatagcatgacttatgttgtgcttccattgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG
 ttttgat  putative branch site (score: 4)
 cttccattgccttt  putative PPT
 aaaattagatcata  TA-rich tract