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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggacaaaaaacaggtcatgcattcttgccgttcagtattttattacacaagaaacataacgaattctgtcgtttgatgttccttttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCA

Basic information

species Oryza sativa
transcript LOC_Os01g09300.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09300.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 5
gtggacaaaaaacaggtcatgcattcttgccgttcag-tattttattacacaagaaacataacgaattctgtcgtttgatgttccttttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCA
               ||||||| ||| || |   | | |||||||   | |||| ||||| |||| | |||||||||||||||| || | ||  ||||||| || ||| |||||||| |||| ||||  ||||| || |||||||| || || ||||| || ||||| ||||||||||||||||||||||| |||||
---------------gtcatgccttcgtgtcagacgggtattttaccccgcaaggaacatgacgagtcctgtcgtttgatgttctttctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCA

upper sequence: LOC_Os01g09300.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G147882_T04 (Zea mays), 3'ss of exon 5
gtggacaaaaaacaggtcatgcattcttgccgttcag-tattttattacacaagaaacataacgaattctgtcgtttgatgttccttttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCA
|||||||| ||||||||||||| ||| || |   | | |||||||   | |||| ||||| |||| | |||||||||||||||| || | ||  ||||||| || ||| |||||||| |||| ||||  ||||| || |||||||| || || ||||| || ||||| ||||||||||||||||||||||| |||||
gtggacaagaaacaggtcatgccttcgtgtcagacgggtattttaccccgcaaggaacatgacgagtcctgtcgtttgatgttctttctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCA

upper sequence: LOC_Os01g09300.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 5
gtggacaaaaaacaggtcatgcattcttgccgttcag--tattttattacacaagaaacataacgaattctgtcgtttgatgttccttttttc-atcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCA
               ||||     |  |  | |  |   | |   |||  | |    | |||||  ||   ||  |  | | | || |||||| ||||||| || | ||  ||||     ||||| | | |||||||||||| |||||||| |||||||| || || ||  ||||||| ||||||||  | || || ||
---------------gtcactggattctatcatcaaacttgtaccatttaaaactgtatataactcatatcgtgatgggttttcccctttttccatcagGTCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCA

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|29638841|gb|CB643850.1|CB643850
EST:     AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGGTGGACAAAAAACAG           
genomic: AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCA-T-T--A--T-G-------A-AGgtggacaaaa
EST: gi|29662625|gb|CB658900.1|CB658900
EST:     AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGGTGGACAAAAAACAG           
genomic: AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCA-T-T--A--T-G-------A-AGgtggacaaaa
EST: gi|25803965|gb|CA759926.1|CA759926
EST:     CCCATAGCCACATTAAGGCTCNTGCNCTATGAAG                         GTAAAGTATCAAATCCTGCAGAGGGAG-TTTTGGAGCAGGTGCCCATTCTG
genomic: CCCATAGCCACATTAAGGCTCCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
EST: gi|33690409|gb|CF318648.1|CF318648
EST:     ATTAAGGCTCCTGCATTATGAAG                         GTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
genomic: ATTAAGGCTCCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
EST: gi|300215975|gb|HO088601.1|HO088601
EST:     GAAATGGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAG                         GTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
genomic: GAAATG-CTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
EST: gi|29678794|gb|CB675069.1|CB675069
EST:     CCTGCATTATGAAG                         GTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
genomic: CCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
EST: gi|29615162|gb|CB620175.1|CB620175
EST:     AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAG                         GTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
genomic: AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
EST: gi|58597848|gb|CK008376.1|CK008376
EST:     AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAG                         GTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
genomic: AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
EST: gi|38473536|gb|CF957668.1|CF957668
EST:     AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAG                         GTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
genomic: AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
EST: gi|27546279|gb|CA767193.2|CA767193
EST:     AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAG                         GTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
genomic: AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
EST: gi|29665424|gb|CB661699.1|CB661699
EST:     CGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAG                         GTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
genomic: CGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
EST: gi|29655813|gb|CB652088.1|CB652088
EST:     AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAG                         GTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG
genomic: AGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTG

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: 64 (upstream exon), 65 (downstream exon)
Score: 22

AGGATTATTGCCCTTGCTCTAAACCTAGAAGAGGACTTCTTTGATAAACCAGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGgtggacaaaa ... ttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattacacaagaaacataacgaattctgtcgtttgatgttccttttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCA
                                     tgttccttttttcatc  CT-rich tract
                                           ttttttcat  TA-rich tract