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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgcttgtttcaccttttaaaatgtatacattttttgtgaataaaagacattgtttatacttctagttatgtctattgcattatatctctgagtacattataatgtctctag

Basic information

species Oryza sativa
transcript LOC_Os12g01140.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.5 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 13
TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgcttgtttcaccttttaaaatgtatacattttttgtgaataaaagacattgtttatacttctagttatgtctattgcattatatctctgagtacattataatgtctctag
||| |||||||| |||||| |    ||||| ||||||||||||||||||||||||||||||||  ||||||||||||| || ||||| |||     ||  ||  ||| |  |   |||   |||| ||             |  ||  | || || | || | |    |||   || | |        ||||||  ||||||
TGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAGgtatga-----gtaacaaatttgatcacaaataacattttagt-------------tacttccatttttaatgattttttccacatctgatttgt-------ctataatacctctag

upper sequence: LOC_Os12g01140.5 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 5'ss of exon 14
TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgcttgtttcaccttttaaaatgtatacattttttgtgaataaaagacattgtttatacttctagttatgtctattgcattatatctctgagtac-attataatgtctctag
||| ||  |||| || || |     || || |||||||||||||||||||||||||||||||   ||||||| |||||||| ||||| |     |    | |  ||      |   ||| ||| | || |||  |  |       ||  ||  |||  ||  ||||||  ||| || | ||| ||| |     |||       
TGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtat-----tcaaattaaattgctgggt---tacttttctagttaatttagca-gccagataagctcttaga-attcctattgt-ttacatgtatgactactacagctatg-------
















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|66913937|gb|CX100785.1|CX100785
EST:     ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG                         GTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
genomic: ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgct ... atgtctctagGTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
EST: gi|29623925|gb|CB628936.1|CB628936
EST:     ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG                         GTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
genomic: ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgct ... atgtctctagGTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
EST: gi|29622723|gb|CB627734.1|CB627734
EST:     ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG                         GTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
genomic: ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgct ... atgtctctagGTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
EST: gi|29672018|gb|CB668293.1|CB668293
EST:     ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG                         GTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
genomic: ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgct ... atgtctctagGTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
EST: gi|87007902|gb|CI296880.1|CI296880
EST:     ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG                         GTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
genomic: ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgct ... atgtctctagGTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
EST: gi|29613611|gb|CB618624.1|CB618624
EST:     ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG                         GTTCACAGAGCTACTGCTGA
genomic: ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgct ... atgtctctagGTTCACAGAGCTACTGCTGA
EST: gi|27334351|gb|CA882802.1|CA882802
EST:     ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG                         GTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
genomic: ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgct ... atgtctctagGTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
EST: gi|29641400|gb|CB646407.1|CB646407
EST:     ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG                         GTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA
genomic: ACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgct ... atgtctctagGTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCA

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: 54 (upstream exon), 66 (downstream exon)
Score: 25

TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgct ... atgtctctagGTTCACAGAGCTACTGCTGAACGCCAAATCCTTGATCTATTAGATCACCCATTCCTTCCAACATTATATGCATCATTTCAG




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