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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgcctgcttctaatgcctatttcttcctcttcgttgtaagagcgcttttttgatctgattatgttttaacgcatctaaataatttttttaactcaagTGCTAGGAACATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCAC

Basic information

species Oryza sativa
transcript LOC_Os02g07490.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 2
gtaactgcctgcttctaatgcctatttcttcctcttcgttgtaagagcgcttttttgatctgattatgttttaacgcatctaaataatttttttaactcaagTGCTAGGAACATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCAC
|||| ||| |||||  || |||    ||    ||  | ||||||  |   |||      | |    || | |    | ||||| | | | |   || | |||||| |||||| | ||||||||||| |||||||| || ||||| ||||||||| | ||||
gtaagtgcttgctttcaacgccgtagtcactgtcgcc-ttgtaaatgtagttt------caggcattgctattgtccgtctaactcactgtg--aattgaagTGCGAGGAACCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCAC

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 2
gtaactg---cctgcttctaatgcc-tatttcttcctcttcg---ttgtaagagcgcttttttgatctgattatgttttaacgcatctaaataatttttttaactcaagTGCTAGGAACATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCAC
|||| ||   | | ||| | | ||| || | | |||   ||    ||||||| |   |||       || |   ||   |     |||||   || || | || | |||||| ||| |||| |||||| |||||||||||||||| ||||| ||||||||||| ||||
gtaagtggtgcttacttttgaggccctagtccgtccctgtcagccttgtaagtgtagtttcagacattggtacagtc--agtctgtctaa--catcttgtgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGCCGTGCCAC
















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|58609065|gb|CK037098.1|CK037098
EST:     AGAAGCGCTGGCTCAGCTCAGTTCACCTCCATCGCAGCTTCCTCTTCATT                         TGCTATGAACATTGAGCTGCTGAGAGCGATAGCTACTCAGGCACCCCCTGC
genomic: AGAAGCGCTGGCTCAGCTCAGTTCACCTCCATCGCAGCTTCCTCTTCATTgtaactgcct ... ttaactcaagTGCTAGGAACATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGC
EST: gi|8594714|gb|AU093252.1|AU093252
EST:     AGAAGCGCTGGCTCAGCTCAGTTCACCTCCATCGCAGCTTCCTCTTCATT                         TGCTAGGAACATTGAGCCGCTGAGAGCGATAG-TACTCAGGCACCCCCTGC
genomic: AGAAGCGCTGGCTCAGCTCAGTTCACCTCCATCGCAGCTTCCTCTTCATTgtaactgcct ... ttaactcaagTGCTAGGAACATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGC

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: 62 (upstream exon), 59 (downstream exon)
Score: 20

GTGTTACGCTTGAGAAGCGCTGGCTCAGCTCAGTTCACCTCCATCGCAGCTTCCTCTTCATTgtaactgcct ... ttaactcaagTGCTAGGAACATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcttttttgatctgattatgttttaacgcatctaaataatttttttaactcaagTGCTAGGAACATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCAC
                                           ttttaac  putative branch site (score: 20)
                                        ttttttt  CT-rich tract
               attatgttttaacgca  TA-rich tract