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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttccctttcaactgaacctgtacattggcgaatttatttcccttttttgtgagtacattctcttgctgctcacacaagttagacaagaaatttggcttgtgtctaactcccttctgctctttgttaccctagGTAAATGAGGAAGAAGCTTCACTCTTCGACATATTATATTTGCTTCTGGCTAGTGTTGTGTTTGTACCATTATTTCAGAAAATACCTGGAG

Basic information

species Oryza sativa
transcript LOC_Os04g58620.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 2
gtatgttccctttcaactgaacctgtacattggcgaatttatttcccttttttgtgagtacattctcttgctgctcacacaagttagacaagaaatttggcttgtgtctaa-ctcccttctgctctttgttacccta----gGTAAATGAGGAAGAAGCTTCACTCTTCGACATATTATATTTGCTTCTGGCTAGTGTTGTGTTTGTACCATTATTTCAGAAAATACCTGGAG
|||   |  | | || |||||| ||  |||   |  ||||         ||||||  |||| |||   || |  |||     ||||   | |||| || |||||  | |||  | ||||   ||| |  || |||||    |||||||||||||||||||||||| ||||||||| | ||||||||||| || |||||| | ||||||||||||||||||||||| |||||||
gtacaatttcct-catctgaacttgctcatcttctgattt-------cattttgt--gtac-ttcgaatgatattcaact--gttatg-atgaaacttagcttgcatgtaaatttccttacactcgtcatttccctattcagGTAAATGAGGAAGAAGCTTCACTTTTCGACATACTGTATTTGCTTCTTGCCAGTGTTATTTTTGTACCATTATTTCAGAAAATCCCTGGAG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 3
gtatgttccctttcaactgaacctgtacattggcgaatttatttcccttttttgtgagtacattctcttgctgctcacacaagttagacaagaaatttggcttgtgtctaactcccttctgctctttgttaccc---tagGTAAATGAGGAAGAAGCTTCACTCTTCGACATATTATATTTGCTTCTGGCTAGTGTTGTGTTTGTACCATTATTTCAGAAAATACCTGGAG
|||   |  | | ||  |||||   || |||   || || ||||    ||  | |  | | ||||   || |                 | | ||  | |||    | ||| | |||| |||||||  || ||     ||||||||||||||||||||||||| ||||||||| |||| ||||||||||| |||||| | ||||||||||||||||||||||| |||||||
gtacaatttcct-catttgaactacta-atttctgatttcattttgtgttcgtctatg-atattcaactgttatg--------------atggaacatagctcacatgtaagttccttatgctcttcattccctattcagGTAAATGAGGAAGAAGCTTCACTTTTCGACATACTATACTTGCTTCTGGCCAGTGTTATTTTTGTACCATTATTTCAGAAAATCCCTGGAG
















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|29674000|gb|CB670275.1|CB670275
EST:     AGATCCCACAACGAGTAAAAAAGCTTATTGAGCTCTTACCTCATCAAGAG                         GTAAATGAGGAAGAAGCTTCACTCTTCGACATATTATATTTGCTTCTGGCT
genomic: AGATCCCACAACGAGTAAAAAAGCTTATTGAGCTCTTACCTCATCAAGAGgtatgttccc ... gttaccctagGTAAATGAGGAAGAAGCTTCACTCTTCGACATATTATATTTGCTTCTGGCT




















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: 57 (upstream exon), 74 (downstream exon)
Score: 8

TATTGAGGAAGTTACCTCCACTGCAAAGCCCATAGTTCGTGAGATGCGAAAGATCCCACAACGAGTAAAAAAGCTTATTGAGCTCTTACCTCATCAAGAGgtatgttccc ... gttaccctagGTAAATGAGGAAGAAGCTTCACTCTTCGACATATTATATTTGCTTCTGGCTAGTGTTGTGTTTGTACCATTATTTCAGAAAATACCTGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagacaagaaatttggcttgtgtctaactcccttctgctctttgttaccctagGTAAATGAGGAAGAAGCTTCACTCTTCGACATATTATATTTGCTTCTGGCTAGTGTTGTGTTTGTACCATTATTTCAGAAAATACCTGGAG
                       gtctaac  putative branch site (score: 8)
                             ctcccttctgctcttt  CT-rich tract
       aagaaattt  TA-rich tract