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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatcctgaccaatttaatgtttgttatgtctacttacctctcaaaatgcatatgtaggtatcaccatgacagtaggtgaacgtttggaatcatg...

Basic information

species Oryza sativa
transcript LOC_Os04g56450.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G056572_T02 (Zea mays), 5'ss of exon 6
GAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatcctgaccaatttaatgtttgttatgtctacttacctctcaaaatgc-atatgtaggtatcaccatgacagtaggtgaacgtttggaatcatg--
|||||||||| ||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||||| ||||||||||| ||||| || ||| | ||||     | || || | | |  | | | |||  |   |  |   | |  |  |      || |  | | || ||    |   | | | | |||  
GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatcta---cgatatattttatactttctttacaaaatgcatattgttctgttcgggaacttccctgtaataggagaattatagtagtattaatgat

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G06250.1 (Glycine max), 5'ss of exon 7
GAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatg-caatcctgaccaatttaatgt-ttgttatgtctact-tacctctcaaaatgcatatgtaggtatcaccatgacagtaggtgaacgtttggaatcatg
|||| ||| | ||||| ||||| |||||||||||||| || |||||||| | |||| | ||||||||||| ||||  ||||| || |||| |||||| | |   ||   | ||   |   || ||   | |  | ||    |    || ||| |  |  | |   ||| | ||  |||| | | ||      |  
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctactatggttagttacgtccattcttgaatatcttatatagttatggattcatctcaacctgtgctcat-atag--ggtgcatggttaagtgtaca

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
GAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatg-caatcctgaccaatttaatgt-ttgttatgtctact-tacctctcaaaatgcatatgtaggtatcaccatgacagtaggtgaacgtttggaatcatg-
|||| ||| | ||||| ||||| |||||||||||||| || |||||||| | |||| | ||||||||||| ||||  ||||| || |||| |||||| | |   ||   | ||  ||   || ||   | |  | ||    |    || ||| |  |  | |   ||| | ||  |||| ||| ||   ||  || 
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctacaatggttagttacatccattcttgaatatgttatatagttatggattcatctcaacctgtgctcat-atag--ggtgcacggttcacatt-tgt

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 5'ss of exon 7
GAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatcctgaccaatt--taatgtttgttatgtctacttacctctcaaaatgcatatgtaggtatcaccatgacagtaggtgaacgtttggaatcatg
|||| ||| | ||||| ||||| |||||||||||||| || |||||||| | |||||| ||||||||||| ||||  ||||| || || | ||| ||       ||     |  ||| | | |||      | || | |||    |    |||| || ||  | | |      |||  |    | || |  || 
GAACTTGGAGGGTTGGGGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCTTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAGgtctggctctgagagttgatagtaaagctagttgacataatttgcatctagcgaattttatgcagttaaaatc-tattccaagggcactcctaggcagaat-

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|8858859|gb|AU096177.1|AU096177
EST:     TTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGNATCCTGAGATTCGG                         GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatc ... tgggtcatagGAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
EST: gi|27547322|gb|CA765327.2|CA765327
EST:     TTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG                         GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatc ... tgggtcatagGAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
EST: gi|66920381|gb|CX107229.1|CX107229
EST:     AACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG                         GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
genomic: AACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatc ... tgggtcatagGAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
EST: gi|24208771|gb|AU225798.1|AU225798
EST:     CAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG                         GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
genomic: CAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatc ... tgggtcatagGAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
EST: gi|86536657|gb|CI176863.1|CI176863
EST:     TGTGGATCCTGAGATTCGG                         TAGCAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTGGCAAGTGATGGG
genomic: TGTGGATCCTGAGATTCGGgtatgcaatc ... tgggtcatagGAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
EST: gi|14981649|gb|BI306327.1|BI306327
EST:     TTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG                         GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatc ... tgggtcatagGAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
EST: gi|5003298|gb|AU068447.1|AU068447
EST:     TTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG                         GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatc ... tgggtcatagGAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGG

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), 73 (downstream exon)
Score: 23

GAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatc ... tgggtcatagGAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG




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