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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtctttgaactaacataattatttgagcttactctgttttatatacagttgatggttaattttgtttttctgttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGAGCCTGAATCATTGTTGTCCTCACCTATACTGAACTTCTACATTAT

Basic information

species Oryza sativa
transcript LOC_Os06g29310.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g29310.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G351786_T01 (Zea mays), 3'ss of exon 7
gttggtctttgaactaacataattatttgagcttactctgttttatatacagttgatggttaattttgtttttctgttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGAGCCTGAATCATTGTTGTCCTCACCTATACTGAACTTCTACATTAT
|||||   || | ||       || || || |||  | ||    | | |||||| || |  | |||| ||  |   || |   ||||||   || |  |||| ||||| || ||| |  |||||| |  ||| |  |||||||||||||| |||||||||||||| ||||||| ||||| ||
gttggcagttaatctggt----ttcttcgatcttcttttg----acacacagttcatcgcca-tttttttcctgccttattcacagGGAACACCTTTGTTCTGTTGAGATTGCTTCTGATGACATCAGATGTTTCCAGCCTGAATCATTGCTGTCCTCACCTATAATGAACTTTTACATCAT
















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|88334047|gb|CI641098.1|CI641098
EST:     TGATGCAATGAAGATACACTATCCTTCATG                         GGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
genomic: TGATGCAATGAAGATACACTATCCTTCATGgttggtcttt ... ttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
EST: gi|88331767|gb|CI640798.1|CI640798
EST:     TGATGCAATGAAGATACACTATCCTTCATG                         GGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
genomic: TGATGCAATGAAGATACACTATCCTTCATGgttggtcttt ... ttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
EST: gi|33793431|gb|CF322595.1|CF322595
EST:     TGATGCAATGAAGATACACTATCCTTCATG                         GGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
genomic: TGATGCAATGAAGATACACTATCCTTCATGgttggtcttt ... ttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
EST: gi|33794144|gb|CF322962.1|CF322962
EST:     TGATGCAATGAAGATACACTATCCTTCATG                         GGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
genomic: TGATGCAATGAAGATACACTATCCTTCATGgttggtcttt ... ttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
EST: gi|88331768|gb|CI640799.1|CI640799
EST:     TGATGCAATGAAGATACACTATCCTTCATG                         GGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
genomic: TGATGCAATGAAGATACACTATCCTTCATGgttggtcttt ... ttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
EST: gi|88573239|gb|CI664810.1|CI664810
EST:     TGATGCAATGAAGATACACTATCCTTCATG                         GGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
genomic: TGATGCAATGAAGATACACTATCCTTCATGgttggtcttt ... ttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
EST: gi|88333541|gb|CI656613.1|CI656613
EST:     TGATGCAATGAAGATACACTATCCTTCATG                         GGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA
genomic: TGATGCAATGAAGATACACTATCCTTCATGgttggtcttt ... ttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGA

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: 70 (upstream exon), 30 (downstream exon)
Score: 12

TGATGCAATGAAGATACACTATCCTTCATGgttggtcttt ... ttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGAGCCTGAATCATTGTTGTCCTCACCTATACTGAACTTCTACATTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttactctgttttatatacagttgatggttaattttgtttttctgttctctgcagGGACACCCCTAATTCTATTGAGCTTTCTTATTCTGACATGAAGTGTCTTGAGCCTGAATCATTGTTGTCCTCACCTATACTGAACTTCTACATTAT
                                ttttgtttttctgttc  CT-rich tract
                            ttaattttgtttttct  TA-rich tract