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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcctattgctttatatatccttgtccggaggctgaatgagcatctctctctctctctctctctctctaaacagctttttttttctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCCAGTAGGCATGTGAAAATCCATACCAAACTTTTGCGTGATCATATAGATA

Basic information

species Oryza sativa
transcript LOC_Os01g57550.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g57550.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G142507_T02 (Zea mays), 3'ss of exon 6
gtgagtc-ctattgctttatatatccttgtccggaggctgaatgagcatctctctctctctctctctctctctaaacagctttttttttctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCCAGTAGGCATGTGAAAATCCATACCAAACTTTTGCGTGATCATATAGATA
||||| | || ||| |   |||     |||   |||||| ||  |            | |||    | |  || | |||||| || || || |||||||| |||||||||||| ||||||||||| |||||||| ||||| ||||||| |||| | |||||||||||||| || ||||  ||| | |||||||||||||
gtgaggcgctgttgttccgtatcgttctgtt--gaggctaaaaca------------cactcctcattttcctgaccagcttgttgttcctgtcttcagATGCTCATGGATGTTCTGGATTTTCTCAGATTGCCAAAGAGGAAGCTGTTCAGTCGACATGTGAAAATCCACACAAAACGATTGTGCGATCATATAGATA

upper sequence: LOC_Os01g57550.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G877077_T01 (Zea mays), 3'ss of exon 5
gtgagtc-ctattgctttatatatccttgtccggaggctgaatgagcatctctctctctctctctctctctctaaacagctttttttttctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCCAGTAGGCATGTGAAAATCCATACCAAACTTTTGCGTGATCATATAGATA
||||||  || |||||| || |     |||   |||||| ||| |   |  |  | ||             || ||||   | || ||||| |||||||| |||||||||||||||||||||||| ||| |||||||||| |||||||  ||| | |||||||||||||| || ||||  |||||||||||||| ||||
gtgagttgctgttgcttcatgtcggtctgtt--gaggctaaatcaaacttccattttc-------------ctgaacaatgtgttgtttctgtcttcagATGCTCATGGATGTCCTGGATTTTCTAAGACTGCCTAAGAGGAAGCTGTTGAGTCGACATGTGAAAATCCACACTAAACGATTGCGTGATCATATTGATA
















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|86430219|gb|CI082642.1|CI082642
EST:     AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88545094|gb|CI474631.1|CI474631
EST:     TGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: TGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88533370|gb|CI460922.1|CI460922
EST:     CTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: CTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88521578|gb|CI449281.1|CI449281
EST:     GTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: GTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|58679934|gb|CK068621.1|CK068621
EST:     AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88541963|gb|CI471267.1|CI471267
EST:     AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|50878563|gb|AF527724.1|AF527724
EST:     AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|29631925|gb|CB636934.1|CB636934
EST:     AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88842012|gb|CI081268.1|CI081268
EST:     AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88542257|gb|CI471575.1|CI471575
EST:     GGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: GGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88552730|gb|CI482765.1|CI482765
EST:     TCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: TCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88828732|gb|CI073602.1|CI073602
EST:     AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|86430910|gb|CI083333.1|CI083333
EST:     AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: AGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88521518|gb|CI449214.1|CI449214
EST:     TATTCTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: TATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88528015|gb|CI456215.1|CI456215
EST:     TGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: TGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
EST: gi|88548461|gb|CI476835.1|CI476835
EST:     ATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACT                         AAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC
genomic: ATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCC

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), 74 (downstream exon)
Score: 9

TCTTAAGAAATCCGATAAGTTGGCCGCTGATGCTTTACTGTACTTCAAAAAGACACGCCATATTATTCTGTATTATGAGGATGTTGTCAGCAATGATACTgtgagtccta ... ctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCCAGTAGGCATGTGAAAATCCATACCAAACTTTTGCGTGATCATATAGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatctctctctctctctctctctctctaaacagctttttttttctttcttcagAAGCTCATGGATGTCCTGGATTTTCTGAGATTGCCTAAGAGAAAGCTGTCCAGTAGGCATGTGAAAATCCATACCAAACTTTTGCGTGATCATATAGATA
                         ctctaaa  putative branch site (score: 9)
       ctctctctctctctct  CT-rich tract
                                    tttttttttctttctt  TA-rich tract