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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagggcttgcaaatcactatgtttcttatttaaaaaattaaactattattttgcaaaaaagcttacatatcaatatttcttgctttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT

Basic information

species Oryza sativa
transcript LOC_Os12g30540.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 22
gtgagggcttgcaaatcactatgtttcttatttaaaaaattaaactattattttgcaaaaaagctt---------------acatatcaatatttcttgctttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT
|| |||| |||||||| | || | | | | || |||| |||| | | ||| | | || | ||||||| ||||||||||||| |||||||||||||||||||||||||||||||||||||||| ||||||| ||||||||||||||||| ||||| |||||||||||||| ||||||
gtaagggattgcaaatgaaactgataaactggtttacatttgaacttcggttttacgttggaactttggttttgaatcaacatacatatgtgtttcttgttttcacttagGTCAAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACATAAACTTGGGTTGGATGATCCATCAAAGATTCGGCTTACATCTCACAATTGTTAT

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 12
gtgagggcttgcaaatcactatgtttc-ttatttaaaaaattaaactattattttgcaaaaaagcttacatatcaatatttcttgctttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT
|| |||| |||||||||| || | | || | | || |||| ||||| | || |||| | | ||||||| |||||| |||||||||||||||||| |||||||||||||||||||||||||||| |||||||| ||||||||||||||||| || || ||||| |||||||| ||||||
gtaagggattgcaaatcaaactgataaactggttttacatttgaactgcagttttgaatcaacttaaacatgttt-tttttcttgttttcacctagGTCGAAGCTTCATACATATGATGATGTTGTTGAGAGAGTTGCACATCAACTTGGGTTGGATGATCCATCAAAGATACGGCTTACGTCTCACAATTGTTAT

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 14
--------------------------------------------------gtgagggcttgcaaatcactatgtttc-ttatttaaaaa--attaaact-attattttgcaaaaaagcttacatatcaatatttcttgctttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT
|| || | || || | | ||||||| | | |||| || | |||||| | |||| || | || | || |||| |||||| | |||| ||| ||||||||||| || |||||||| || | |||||||| ||||||||||||| ||||| || |||||| | |||||||| ||
gtaagcatcttggaacttattgggggcaaattgttaagtttgatactatttagattttttactaacgtgcatatgtagttatttatagataattatgcttagcattttgtcctcagtcttatattttcccatatattaatttc---tagGTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTCTGGATGATCCATCCAAAATACGGCTTACACCACACAACTGCTAC

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 3
----------------------gtgagggcttgcaaatc----actatgtttcttatttaaaaaattaaact-attattttgcaaaaaagcttacatatcaatatttcttgctttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT
| | | |||| ||||| | || |||| || ||| || | ||| || | |||| | | || | || ||| |||||| | |||| ||| ||||||||||| || |||||||| || | |||||||| ||||||||||| || ||||| || |||||| | |||||||| ||
gtaagcatcttgaaacttacatgggcaaattgttaaatttgatactatttaaattttttactaatttatgctgagcattctgtccttagtcttatactttcccatatgttaacttc---tagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTTTGGATGATCCGTCCAAAATACGGCTTACACCACACAACTGCTAC

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 22
gtgagggcttgcaaatca---ctatgtttcttatttaaaaaattaaactattattttgcaaaaaagcttacatatcaatatttcttgctttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT
|| || | | ||| | || |||| | | | | || || || |||| | | | | | | | || || ||||| ||||| || | ||||||||||||||| || ||||| || || |||||| |||||||||||||| ||||| | ||||||||||||||||| |||
gtaagtacatatccatctaatcagtggttctgacatgatgag--aatctgttgtttttatttgatgtctgtaaccctctttcatttatattattcaagGTCAAAGCTACACAATTATGATGATGTTGTGGAAAGAGTGGCTCGTAGACTTGGTTTGGATGATCCATCCAAAATCAGACTTACATCTCACAACTGCTAT

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 22
gtgagggcttgcaaatcactatgtttcttatttaaaaaattaaactattattttgcaaaaaagct--tacatatcaatatttcttgctttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT
|| || || |||||| | ||| || || | |||| | || ||| | |||| | ||||| ||| | ||||| |||||| |||||||||||| || || || ||||| || || || ||||| |||||||||||||| ||||| | || |||||||||||||||||
gtaagtgc--agaaatcaat-tgtaactaatc---agcattatgattatagtttatttactagctggtgcatatgaatgtcc-------------agGTCAAAGCTTTTTACTTATGATGACGTGGTAGAAAGAGTAGCTCGTCAGCTTGGTTTGGATGATCCATCCAAAATCAGGCTCACATCTCACAACTGTTAC

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|29625340|gb|CB630351.1|CB630351
EST:     CACTTCCGGTCTTTGGAGAA-CCAAAGGAGGATGATTTTTGTTTGGAATT                         GTCGAAGCTTCATACTTATGATG
genomic: CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATTgtgagggctt ... tttcacttagGTCGAAGCTTCATACTTATGATG
EST: gi|25799966|gb|CA755927.1|CA755927
EST:     CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATT                         GTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACT
genomic: CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATTgtgagggctt ... tttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACT
EST: gi|58678676|gb|CK067363.1|CK067363
EST:     CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATT                         GTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACT
genomic: CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATTgtgagggctt ... tttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACT
EST: gi|29637181|gb|CB642190.1|CB642190
EST:     CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATT                         GTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACT
genomic: CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATTgtgagggctt ... tttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACT
EST: gi|29614412|gb|CB619425.1|CB619425
EST:     CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATT                         GTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACT
genomic: CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATTgtgagggctt ... tttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACT
EST: gi|2309706|gb|C25861.1|C25861
EST:     CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATT                         GTCGGAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGNCAACT
genomic: CACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATTgtgagggctt ... tttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACT

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: 56 (upstream exon), 68 (downstream exon)
Score: 30

GTGGTGCACTTCCGGTCTTTGGAGAAACCAAAGGAGGATGATTTTTGTTTGGAATTgtgagggctt ... tttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaactattattttgcaaaaaagcttacatatcaatatttcttgctttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT
                     agcttac  putative branch site (score: 30)
 tttcttgctttcactt  putative PPT
 tattattttgcaaaaa  TA-rich tract