Sequence
atgc intronic sequence ATGC exonic sequencegtattacattctatgcatctgtgttacacactaaattaccaatgaccttcaccactccttcaatggatcatttccagcatccatctatcagttcaccttttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g28570.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 10
gtattacattctatgcatctgtgttacacactaaattacc-aatgaccttcaccact------------ccttcaatggatca--tttccagcat--------ccatctatcagttc-accttttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
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gtcttccattttgtgcccttctatcgcacaacaagttacctagtagcttctgtcgttgaaatgagatcatctgcagcatattaaatttgaaatatagttatgcttgcctgtcagtactggtttttatctttgttttttttctcgtgaagGTTCCAGCCAAACATCTTCTTCCAGTGCCAAGACCAGACCCTGAGGTTGTTGCAATGTTGACATCAGGACTGACTGCATCAATTAGTCTTGAAAAG
upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G368058_T01 (Zea mays), 3'ss of exon 5
gtattacattctatgcatctgtgttacacactaaattaccaatgaccttcaccactccttcaatggatcatttccagcatccatctatcagttcaccttttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
|| || || | | ||| | | |||| || | | || ||||| || | ||| || | || | | |||||| |||| ||| || ||||||| |||| |||| |||||||||||||| |||||||| ||||||||||||||||||||||||||||| || || || ||||| |||
----------------tcctccgt--caaatgagattttctctaacctcttgcattttgggcacc-attatttctgacaataacatatttttttgctttat------atatctttctgatgtaagATTTCAGCCAAAAGTCTTATTCCAGTGCCAAGACCAGACCCAGAGGTGGTTGCTATGCTAACATCAGGATTGACTGCATCCATCGCTCTTGAAAAG
upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA02G15070.1 (Glycine max), 3'ss of exon 10
-------------------------------------------------------gtattaca--ttctatgcatc---tgtgttacacactaaattaccaatgaccttcaccactccttcaatggatcatttccagcatccatctatcagttcaccttttgactttacatcttta-tgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
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gtgggcagtgcttaagataatgttttatatttttcctttcatattaatgacttaattattggagtttccatgtaccacttatttagaaaaccatgtgtttggttat-taagttgatctgataatgatactgtgatgatatttat-tatgatgtaagttattgaagctgtcttgttacttgggatagATTCCTTCAAAACATGCTCTTCCGGTGCCTAGACCAGATCCTGAAGTTGTTGCCATGCTTACATCGGGATTGACTGCCTCAATTGCTCTAGAAAAG
upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G49670.1 (Arabidopsis thaliana), 3'ss of exon 10
gtattacattctatgcatctgtgttacacactaaattaccaatgaccttcaccactccttcaatggatcatttccagcatccatctatcagttcaccttttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
| || | |||||| | |||| | || | | || ||| || ||||| | | | ||| | | ||| |||| | ||| | | |||||| ||||||| || ||||||||||||||||| || ||||| ||||| || || ||||| ||||| | ||| |||||||| |||
------------------gtatgagaactactaaaccat--atgagcaaca----------agttgacatttttcaaggct------tcagtg-atcatgtgaacctgtctgttttggattta-gGTATCTTCTAAGCATGTTCTTCCTGTTCCAAGACCAGATCCAGAAGTTGTTGCCATGCTTACCTCGGGATTAACTGCATTAATCGCCCTTGAAAAG
upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv03s0063g00610.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------------------------------gtattacattctatgcatctgtgttacacactaaattaccaatgaccttcaccactccttcaatggatcatttccagcatccatctatcagttcacctt--ttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
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gtatactaccttaatatttttgcttttaatgttctacagggttggtgtcattattttgtttattttttaattcaattgctacttgatcataat-tttgttaataattaagttacctatcaaaaatgttaataattaaatttgtcggagttgaccccttttttttgc-atgttagGTTCCTTCCAAGCACATCCTTCCCGTGGCAAGACCAGATCCAGAAGTTGTTGCGATGCTAACCTCAGGACTTACAGCATCAATTGCTTTAGAAAAGMapped 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|58684560|gb|CK073247.1|CK073247EST: CTTATGACTTTTGGGG-CTATTCTGAA-TTACTCAG GTTCCAGCCAAGCATCTTCTTCCGGTG-CAAGAGCAGATCCAGAGGTCGTT
genomic: CTTATGATTTTTGGGGCCTATTCTGAATTTACTCAGgtattacatt ... atgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTT
EST:
gi|88405965|gb|CI591360.1|CI591360EST: CAGTCCTGTAGCCCTTATGATTTTTGGGGCCCTATTCTGAATTTACTCAG GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATC-AGAGGTCGTT
genomic: CAGTCCTGTAGCCCTTATGATTTTTGGGGCC-TATTCTGAATTTACTCAGgtattacatt ... atgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTT
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),
71 (downstream exon)
Score:
32TGTGGGCATCGTTGCATCTGTTGGAGATTCAGTGAACCATATTAAAGTTGGCAGTCCTGTAGCCCTTATGATTTTTGGGGCCTATTCTGAATTTACTCAGgtattacatt ... atgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccagcatccatctatcagttcaccttttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
ttttgac putative branch site (score: 32)
tctttat putative PPT
atctttatgattaaa TA-rich tract