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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttgtttttctctctttctggaagtatcttaatggttctgccctatatgtgattacagtcatggtgaaaacctctctttcgtgattttccagGGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCATACACTGATTACTCATTGGATATGGGGTTAATTACAAAATCACAGTTTA

Basic information

species Oryza sativa
transcript LOC_Os07g29620.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g29620.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G018950_T01 (Zea mays), 3'ss of exon 4
gttttgtttttctctctttctggaagtatcttaatggttctgccctatatgtgattacagtcatggtgaaaacctctctttcgtgattttccagGGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCATACACTGATTACTCATTGGATATGGGGTTAATTACAAAATCACAGTTTA
| ||| ||| |||| | |||||| | | |||| | | | | | |||||||| |||| |||| ||| |||||||||||||||||||| || |||| |||||||||||||| |||||||||||| |||||||| ||||||||||||| |||||||||||| |||| ||||
---gtttttctctttcttggttgaagtactatgttttttctttgttgaagatagt-attttcatggtgtggtcctcactttatatgatttacagGGTTTTGCTATTGGCAACGGACTAACAGATCCAGCAATACAGTACAAGGCATACCCTGATTACGCATTGGATATGGGATTAATTACAAAAACACAATTTA

upper sequence: LOC_Os07g29620.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G30160.1 (Glycine max), 3'ss of exon 4
gttttgtttttctctc--tttctggaagtatcttaatggttctgccctatatgtgattacagtcatggtgaaaacctctctttcgtgattttccagGGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCATACACTGATTACTCATTGGATATGGGGTTAATTACAAAATCACAGTTTA
|| || | |||| || | | | | | | | | | | | | | | | ||| | | | | | | ||||||||||||||||||||||||||||| |||| | ||| || ||| ||||||| || |||||| |||| || | ||| |||||| ||| | | | |
gtctttactatctcataacttttagtataactatgaaaggttaat--tgttttttttcttcattgtattgattccgttgatcccatatataaacagGGTTTTGCTATTGGCAATGGGTTAACCAATCCTGAAATTCAGTACCAGGCATATACAGATTACGCATTAGACAGGGGACTAATTAAAAAGGCTGATTATG

upper sequence: LOC_Os07g29620.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G08500.1 (Glycine max), 3'ss of exon 6
--------gttttgtttttctctctttctggaagtatcttaatggttctgccctatatgtgattacagtcatggtgaaaacctctctttcgtgattttccagGGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCATACACTGATTACTCATTGGATATGGGGTTAATTACAAAATCACAGTTTA
|| || | || ||||| | | || || | || ||| | | || | | || | | | | | |||||||||||||||||| ||||||||||| |||| ||||| |||||| |||||| | |||| | || || | || |||||||||| | ||
tataaacctcgaggtcttacactatttctagtatataatttata-taatgaattattttttcttgcttttgcc-tgtattgattcatatgatataacaccagGGTTTTGCTATTGGTAATGGGTTAACAAATCCTGCAATTCAATACCCAGCATACCCAGATTTTGCGTTAGACAACGGAATAATTACAAAGGCTGCGTACG

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|29639499|gb|CB644508.1|CB644508
EST:     GAGTGTACAAGGGGAACAAGAACAGTGAGGGCATTCACATCAATTTGAAG                         GGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCA
genomic: GAGTGTACAAGGGGAACAAGAACAGTGAGGGCATTCACATCAATTTGAAGgttttgtttt ... gattttccagGGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCA
EST: gi|29669656|gb|CB665931.1|CB665931
EST:     GAGTGTACAAGGGGAACAAGAACAGTGAGGGCATTCACATCAATTTGAAG                         GGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCA
genomic: GAGTGTACAAGGGGAACAAGAACAGTGAGGGCATTCACATCAATTTGAAGgttttgtttt ... gattttccagGGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCA
EST: gi|29667652|gb|CB663927.1|CB663927
EST:     GAGTGTACAAGCGGAACAAGAACAGTGAGGGCATTCACATCAATTTGAAG                         GGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCA
genomic: GAGTGTACAAGGGGAACAAGAACAGTGAGGGCATTCACATCAATTTGAAGgttttgtttt ... gattttccagGGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCA

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: 70 (upstream exon), 75 (downstream exon)
Score: 72

TATTACTGGGGAATCGTATGCTGGACACTATATTCCTGCCTTTGCAAGTCGAGTGTACAAGGGGAACAAGAACAGTGAGGGCATTCACATCAATTTGAAGgttttgtttt ... gattttccagGGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCATACACTGATTACTCATTGGATATGGGGTTAATTACAAAATCACAGTTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccctatatgtgattacagtcatggtgaaaacctctctttcgtgattttccagGGTTTTGCTATTGGCAATGGGTTAACGGATCCAGCAATACAATACAAGGCATACACTGATTACTCATTGGATATGGGGTTAATTACAAAATCACAGTTTA
                                               ttttcc  CT-rich tract
 tatatgt  TA-rich tract