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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagttcaaagatcctgcacaaaggggtgctgtcatattcccatttatcattatttttcccataaattcataactatacatcgcattaatacggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCATCCAATACTGGATTTCTTTTACTATATG

Basic information

species Oryza sativa
transcript LOC_Os03g36790.3
intron # 8
splice site 3'
intron type U2

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|88218607|gb|CI218456.1|CI218456
EST:     GTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: GTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|88833207|gb|CI076690.1|CI076690
EST:     GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|14192198|gb|AU184409.1|AU184409
EST:     ATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: ATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|218497390|gb|FG957738.1|FG957738
EST:     GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCCTCATTTGATCCTGATCTATCTCTT
genomic: GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTT
EST: gi|86434389|gb|CI094732.1|CI094732
EST:     GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|27547069|gb|CA765194.2|CA765194
EST:     GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|86489176|gb|CI131809.1|CI131809
EST:     GTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: GTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|86417672|gb|CI031881.1|CI031881
EST:     GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|89179011|gb|CI043516.1|CI043516
EST:     GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|86833244|gb|CI334839.1|CI334839
EST:     TCTTGATAAAATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: TCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|88223214|gb|CI223063.1|CI223063
EST:     GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|12623092|gb|AU173305.1|AU173305
EST:     TTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: TTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
EST: gi|87012849|gb|CI297076.1|CI297076
EST:     GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTG                         GTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT
genomic: GGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCAT

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: 67 (upstream exon), 53 (downstream exon)
Score: 21

GTTGGGACTGTGACAGCAATTTGCTTCACATGTTTCTTGATAAGATGCATTGTGgtgagtgtat ... acggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCATCCAATACTGGATTTCTTTTACTATATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcattatttttcccataaattcataactatacatcgcattaatacggtgatagGTGGCGATGTCATCATTTGATCCTGATCTATCTCTTGAGGTTTTGGATCATCCAATACTGGATTTCTTTTACTATATG
                ataaattcataactat  TA-rich tract