Sequence
atgc intronic sequence ATGC exonic sequencegttctgaacagaagcttatttgactattgttctggattttgtttgcttgaaaagagaactaacagtcatttggtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATGGTAGATATCAACATGACATCGGCAATACTGTTTGTTGTTATTGCATCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g57710.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 5
gttctgaaca--gaagcttatttgactattgttctggattttgtttgcttgaaaaga--gaactaacagtcatttggtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATGGTAGATATCAACATGACATCGGCAATACTGTTTGTTGTTATTGCATCTT
||||| ||| || ||| ||||| | | || ||||| | |||||||| | | ||| |||| || | |||||||| | |||| ||| |||||| ||| |||| ||||||||||| |||||||||||||||||| ||| |||||||||||||| || |||||||| |
gttctaaaccccaaatcttgtttgatttctattgctagttttgcgtacttgaaaaaaagggactgacaggttcaatacttgt-tagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATGGTAGATATCAACATGGTATCCGCAATACTGTTTGTGGTGATTGCATCAT
upper sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------gttctgaacagaagcttatttgactattg------------ttctggat------tttgtttgcttgaaaagagaactaacagtcatttggtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATGGTAGATATCAACATGACATCGGCAATACTGTTTGTTGTTATTGCATCTT
|| ||| || | || || | ||||| || |||||| | | | || || ||| | ||||||||| || | |||| ||||| |||||||||||| ||||| |||||||||| |||||| ||| | || |||||||| || || || |
gtaaacttctccttagttactgttatttccatctcttttgaggagggaactccttactcatgggttaagaatcctttctgaatgatccatttgttcttccattgaatgtatggactgttttttttatcttgtagGATGCTTCAGATGAGTTTCTAAGTACAGAGGGCACTGGTTCTAGTGGTATGGTGGATATCAACACGACATCAGCAGTTCTTTTTGTTGTGATCGCTTCATMapped 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|87006789|gb|CI285823.1|CI285823EST: CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAG GATGGCCATGAAAGCTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
genomic: CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca ... gtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
EST:
gi|300216268|gb|HO088053.1|HO088053EST: CTCGAG-AGCAGTTATTGAACACGAGAAGCTTCTAAAG GATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
genomic: CTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca ... gtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
EST:
gi|29677466|gb|CB673741.1|CB673741EST: CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTACAG GATGGCCATGACAGTTCACT
genomic: CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca ... gtttatgtagGATGGCCATGAAAGTTCACT
EST:
gi|29623066|gb|CB628077.1|CB628077EST: CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAG GATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
genomic: CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca ... gtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
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:
72 (upstream exon),
73 (downstream exon)
Score:
29GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca ... gtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATGGTAGATATCAACATGACATCGGCAATACTGTTTGTTGTTATTGCATCTT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttctggattttgtttgcttgaaaagagaactaacagtcatttggtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATGGTAGATATCAACATGACATCGGCAATACTGTTTGTTGTTATTGCATCTT
aactaac putative branch site (score: 29)
attttgttt TA-rich tract