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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgttacacacctagatcttctaatctatcctagcacaattatgcattgagtataacatggaaaacctattataattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG

Basic information

species Oryza sativa
transcript LOC_Os05g04340.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 5
gtaacg-ttacacacctagatcttctaatctatcctagcacaattatgcattgagtataacatggaaaacctattataattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG
|||| | |||| |  || |   || |   |    |  | | || |        |   |||||||  |||||| ||   ||| |||||| || ||||| ||||| ||||||||||||| |||||| ||||| |||||||| || ||||| |||||||| |||
gtaaagcttactctgctgggagttgttgacagatcctgtataactgcatgacaatagtaacatgtcaaacct-ttgcgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGGGACATTAAGCCGCAAAATCTCCTG
















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|88742984|gb|CI766492.1|CI766492
EST:     AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAG                         ATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
genomic: AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgtaacgttac ... taattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
EST: gi|58679859|gb|CK068546.1|CK068546
EST:     AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAG                         ATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
genomic: AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgtaacgttac ... taattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACA-G
EST: gi|58671594|gb|CK060280.1|CK060280
EST:     AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAG                         ATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
genomic: AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgtaacgttac ... taattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
EST: gi|66928190|gb|CX115038.1|CX115038
EST:     AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAG                         ATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
genomic: AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgtaacgttac ... taattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
EST: gi|29630931|gb|CB635940.1|CB635940
EST:     AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAG                         ATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
genomic: AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgtaacgttac ... taattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
EST: gi|58690705|gb|CK079392.1|CK079392
EST:     AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAG                         ATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
genomic: AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgtaacgttac ... taattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
EST: gi|88356165|gb|CI627613.1|CI627613
EST:     AGATGAACCAACGCATGCCATTGATATATGCAAAAATATACATGTATCAG                         ATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
genomic: AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgtaacgttac ... taattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
EST: gi|29629558|gb|CB634567.1|CB634567
EST:     AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAG                         ATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG
genomic: AGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgtaacgttac ... taattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGG

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: 51 (upstream exon), 72 (downstream exon)
Score: 13

GCTTGAGTATGTGCCAGAGACTGCTCACCGTGTAATTAAACATTACAACAAGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgtaacgttac ... taattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctagcacaattatgcattgagtataacatggaaaacctattataattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG
                       gtataac  putative branch site (score: 13)
                                  aaaacctattataatt  TA-rich tract