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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaatataacagtggtgatactctcgccagaggatcatccttttttattatgtacaaactcgtggcaccagtttgttcatctatgcatatccttgtccatattgctagctagagcagttcttaattatgtcacttacatatgccattttctttttgttgactaacaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGCGACATCTACTGATGGTGATCTTCTAGTATCATGTGGTGTTGACTGCAC

Basic information

species Oryza sativa
transcript LOC_Os01g13730.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13730.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G590033_T01 (Zea mays), 3'ss of exon 4
gtactaatataacagtggtgatactctcgccagaggatcatccttttttattatgtacaaactcgtggcaccagtttgttcatctatgcatatccttgtccatattgctagctagagcagttcttaattatgtcacttacatatgccattttctttttgttgactaacaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGCGACATCTACTGATGGTGATCTTCTAGTATCATGTGGTGTTGACTGCAC
                                     |  | ||    ||||  | || | ||| |  |      ||  ||||||    |||||  | | |||  |  | | |   | |||| |  || || |  | | | |||     | |  ||||    || ||  | |||||||||||||| || |||||||| || || ||||||||||| || |||||  | ||||| || |||||||||||||| ||||||||||| |||||||||||
------------------------------------gtactgctacagtattggggactacctcattcc------ttaatcatctg---atatctgt-ttcatcct-tttgttcttggagttat--atcatatttcatgcttatatttgtgtgatttttacaac-aatgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAACAACATCCACAGATGGTGATCTTCTTGTATCATGTGGCGTTGACTGCAC
















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|29635042|gb|CB640051.1|CB640051
EST:     ATATTCGTCTGTGGGACATTGCTGCAAG                         GAAGACAGTCTGCCAGTTCCCTGGACATCAAGGTGCTGTGAGGGGTTTGGC
genomic: ATATTCGTCTGTGGGACATTGCTGCAAGgtactaatat ... acaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGC
EST: gi|29635043|gb|CB640052.1|CB640052
EST:     ATATTCGTCTGTGGGACATTGCTGCAAG                         GAAGACAGTCTGCCAGTTCCCTGGACATCAAGGTGCTGTG
genomic: ATATTCGTCTGTGGGACATTGCTGCAAGgtactaatat ... acaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTG
EST: gi|29634783|gb|CB639792.1|CB639792
EST:     ATATTCGTCTGTGGGACATTGCTGCAAG                         GAAGACAGTCTGCCAGTTCCCTGGACATCAAGGTGCTGTGAGGGGTTTGGC
genomic: ATATTCGTCTGTGGGACATTGCTGCAAGgtactaatat ... acaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGC
EST: gi|58676759|gb|CK065446.1|CK065446
EST:     ATATTCGTCTGTGGGACATTGCTGCGAG                         GAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGC
genomic: ATATTCGTCTGTGGGACATTGCTGCAAGgtactaatat ... acaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGC
EST: gi|58666954|gb|CK055640.1|CK055640
EST:     ATATTCGTCTGTGGGACATTGCTGCAAG                         GAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGC
genomic: ATATTCGTCTGTGGGACATTGCTGCAAGgtactaatat ... acaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGC
EST: gi|58692216|gb|CK080903.1|CK080903
EST:     ATATTCGTCTGTGGGACATTGCTGCAAG                         GAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGC
genomic: ATATTCGTCTGTGGGACATTGCTGCAAGgtactaatat ... acaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGC

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: 28 (upstream exon), 69 (downstream exon)
Score: 19

ATATTCGTCTGTGGGACATTGCTGCAAGgtactaatat ... acaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGCGACATCTACTGATGGTGATCTTCTAGTATCATGTGGTGTTGACTGCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaattatgtcacttacatatgccattttctttttgttgactaacaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGCGACATCTACTGATGGTGATCTTCTAGTATCATGTGGTGTTGACTGCAC
                                        gactaac  putative branch site (score: 19)
                          attttctttttgtt  TA-rich tract