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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctcttcttattccctttcccctccactgtccatcctttataagtgttgataatcattttactatctttctgtcagGTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGTCTTGAAAAGGACAGCAT

Basic information

species Oryza sativa
transcript LOC_Os08g10600.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10600.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G155729_T01 (Zea mays), 3'ss of exon 11
gtatgtctcttcttattccctttcccctccactgtccatcctttataagtgttgataatcattttactatctttctgtca--gGTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGTCTTGAAAAGGACAGCAT
||||   || |     | ||  ||||||||    |  || || |||| |  || | |||  | | | |   ||| |||||  | | ||| ||||||||||||||||||||||||| || ||||| ||||| |||||||||||||| |||||
gtataattcctacacctgcc--tcccctcc----tatatactatataggcattaacaattgtgt-atttcttttatgtcatagATCTGCTTGCATATGTTTACTTTGGATTTTCTGAACCAAGTGACAAACAGTCTTGAAAAGGATAGCAT
















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|163919868|gb|EG711498.1|EG711498
EST:     CTACTGAAATAAATCAAGGCACAGGGCGCCTTCGTTATTGTTGGAGCAAT                         GTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGT
genomic: CTACTGAAATAAATCAAGGCACAGGGCGCCTTCGTTATTGTTGGAGCAATgtatgtctct ... tttctgtcagGTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGT
EST: gi|29685401|gb|CB681676.1|CB681676
EST:     CTTCGTTATTGTTGGAGCAAT                         GTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGT
genomic: CTTCGTTATTGTTGGAGCAATgtatgtctct ... tttctgtcagGTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGT
EST: gi|29674853|gb|CB671128.1|CB671128
EST:     GTTGGAGCAAT                         GTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGT
genomic: GTTGGAGCAATgtatgtctct ... tttctgtcagGTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGT
EST: gi|29616665|gb|CB621677.1|CB621677
EST:     CTACTGAAATAAATCAAGGCACAGGGCGCCTTCGTTATTGTTGGAGCAAT                         GTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGT
genomic: CTACTGAAATAAATCAAGGCACAGGGCGCCTTCGTTATTGTTGGAGCAATgtatgtctct ... tttctgtcagGTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGT
EST: gi|3767528|gb|AU031622.1|AU031622
EST:     CTACTGAAATAAATCAAGGCACAGGGCGCCTTCGTTATTGTTGGAGCAAT                         GTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGT
genomic: CTACTGAAATAAATCAAGGCACAGGGCGCCTTCGTTATTGTTGGAGCAATgtatgtctct ... tttctgtcagGTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGT

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: 44 (upstream exon), 68 (downstream exon)
Score: 8

GGGTGGGCCTCTTTCTGTAGTTGAGTACAGTGAAATGGATGCAGCTATGACTACTGAAATAAATCAAGGCACAGGGCGCCTTCGTTATTGTTGGAGCAATgtatgtctct ... tttctgtcagGTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGTCTTGAAAAGGACAGCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccactgtccatcctttataagtgttgataatcattttactatctttctgtcagGTATGCCTGCATATGTTTACTTTGGATTTTCTTAATCAAGTAACAAATAGTCTTGAAAAGGACAGCAT
                       tgttgat  putative branch site (score: 8)
                                   ttttactatctttct  putative PPT
                            ataatcattttactat  TA-rich tract