Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgaattgttgctaatttgatgatcagattgatgctgcagttcatttaagttatggtggtattaagcaatattctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g39220.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 4
gtttgtgaattgttgctaatttgatgatcagattgatgctgca------gttcatttaagtt-----atggtggtattaagcaatattctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG
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-------gtttgtagctgatttgatgattatactacactcgcataatgaatttgtgggaggtcttgagtaatggtttgaagcaatgtggtaacacagATAATACAGCATGTGCTTCTAGATATGCCTGGGCTTGCATTCTTCACAACATATGCACTTCTAGTGCTCTTCTGGGCAGAGATTTATTATCAG
upper sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 3
gtttgt----gaattgttgctaatttgatgatca---gattgatgctgcagttcatttaagttatggtggtattaagcaatattctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG
|||||| || ||| | | || || || ||| || | || ||| | |||| | ||||||| | |||| |||||| | |||||||||||||| |||||||||||||| |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||
gtttgtaactgatttgattattatactatactcgtgtgatgaatttgttggaggtctttagtactaatggtttgaagcaatgtggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAG
upper sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G28990.1 (Glycine max), 3'ss of exon 3
----------------------------------------gtttgtgaat----tgttgctaatttg--atgatcagattgatgctgcagttcatttaagttatggtggtattaagcaatattctacc-gcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG
||| |||| | || ||||||| || || ||| | | | | | | ||| | | || | | |||| ||||||| | | || || |||| | || || ||||| || || |||||||||||||| || |||||||| |||||||||||||||
gtattggagtatagggaatgtggcatttatttttgagttattttttgaacctaatattaataatttgttattttctaattagaatgtgattagactcacttaatgctcactctgcatttgcttgtgtttgtagATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTATCAG
upper sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G01360.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------gtttgtgaattgttgctaatttgatgatcagattg-atgctgcagttcatttaagttatggtggtattaagcaatattctac---cgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG
| || | |||| | ||| || || ||| | || ||| | | |||| | || | || | |||| ||||||| | | || || |||| | || || ||||| || || |||||||||||||| || |||||||| ||||||||||| |||
gtattcgagtatagggaatggaatgtaacatttaatttgagtaattttttcttaacataagattagttgtttatt--attttctaattacagaatgtggttagactcacttatactcactcactgcgtttgcttatgtttgtagATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTACCAGMapped 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|29664023|gb|CB660298.1|CB660298EST: AAATGTGCAGCTCATACATCCAGAG ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACG
genomic: AAATGTGCAGCTCATACATCCAGAGgtttgtgaat ... tctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACG
EST:
gi|218501789|gb|FG963428.1|FG963428EST: GATCCATAGTGTTTGTGCTGCGACGAAATGTGCAGCTCATACATCCAGAG ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACG
genomic: GATCCATAGTGTTTGTGCTGCGACGAAATGTGCAGCTCATACATCCAGAGgtttgtgaat ... tctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACG
EST:
gi|29663945|gb|CB660220.1|CB660220EST: ACGAAATGTGCAGCTCATACATCCAGAG ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACG
genomic: ACGAAATGTGCAGCTCATACATCCAGAGgtttgtgaat ... tctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACG
EST:
gi|218494016|gb|FG950655.1|FG950655EST: GATCCATAGTGTTTGTGCTGCGACGAAATGTGCAGCTCATACATCCAGAG ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACG
genomic: GATCCATAGTGTTTGTGCTGCGACGAAATGTGCAGCTCATACATCCAGAGgtttgtgaat ... tctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACG
EST:
gi|218483378|gb|FG949318.1|FG949318EST: GATCCATAGTGTTTCCCCTGCGACGAAATGTGCAGCTCATACATCCAGAG ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACG
genomic: GATCCATAGTGTTTGTGCTGCGACGAAATGTGCAGCTCATACATCCAGAGgtttgtgaat ... tctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACG
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:
53 (upstream exon),
74 (downstream exon)
Score:
64TGCGATCCATAGTGTTTGTGCTGCGACGAAATGTGCAGCTCATACATCCAGAGgtttgtgaat ... tctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgatgctgcagttcatttaagttatggtggtattaagcaatattctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG
gattgat putative branch site (score: 64)
ttctacc putative PPT
ttcatttaagttat TA-rich tract