Sequence
atgc intronic sequence ATGC exonic sequencegtaattttctacctcctctttctgttatcaatgttttcatttcaaagacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttgtctatattctgtactaaggtttttttcaatataatctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g29450.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G464000_T02 (Zea mays), 3'ss of exon 7
gtaattttctacct-cctctttctgttatcaatgttttcatttcaaag----acattttacttcactttgcaacatttagtttttgttatcatgagcaatctttgtctatattctgtactaaggtttttttcaatataatctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
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gtaattttctttcaatctttgtttttcctcaatgacttcactcctgattgataaatgtttatttatttcacagca----gatttcataa----aagcaatgttt-cctctattcaaaactaagaattttc-caatatggttgatgcagAATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATG
upper sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
gtaattttct----acctcctctttctgttatcaatgttttcatttcaaagacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttgtctatattctgtactaaggtttttttcaatataatctat-gcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
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gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttt-tagtctgttttaggtgccgtgacaaataaacttt-tcgccactctaaactaagaattttc-caacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
upper sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 7
gtaattttctacctcctctttctgttatcaatgttttcatttcaaagacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttg--tctatatt-ctgta-ctaaggtttttttcaatataatctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
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--------------------------------------------aaaaaaaactattgtattc--gagaattttatttttcaca-catgctgaactctgggatttgtgttgctatatctataaattaccatgctgtgttattttcagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG
upper sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 6
gtaattttctacctcctctttctgttatcaatgttttcatttcaaa---gacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttgtctatattctgtactaaggtttttttcaatataatctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
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-------------------gtttgtc--caatatttttatcttataattgacaaaccttttcatactg-accatcaaattaataatttca----cattctatgctcatcttatttggcatggcctttgt----------tcttcagAATGCATTGCGGCAGCAAAGATTTGTACGCGAAGTTACAATACAGTACAACCTCTGCAATGAACCATG
upper sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 7
gtaattttctacctcctctttctgttatcaatgttttcatttcaaagacattttac---ttcactttgcaacatttagtttttgttatcatgagcaatctttgtctatattctgtactaaggtttttttcaatataatctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
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-------------------gtttgtc--caatatctttaactgagaatcaacaaaccttttcatattg-accatcggattaataatttca----cattctatgctcatcttatttggtgtggccttcgt----------tcttcagAATGCATTGCGGCAGCAAAGATTTGTACGTGAAGTTACAATACAGTACAACCTCTGCAATGAACCTTG
upper sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 8
gtaattttctacctcctctttctgttatcaatgttttcatttcaaagacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttg--tctatatt-ctgta-ctaaggtttttttcaatataatctatgc--agAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
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---------------------------------------------agaaaaactattgtatt---caagaatttattttccaca-catgttgaactctgggatttgtgttgctatatctagaaattaccatgatgtctgttatttttagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCATG
upper sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G08450.3 (Arabidopsis thaliana), 3'ss of exon 8
gtaattttctacctcctctttctgttatcaatgttttcatttcaaagacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttgtctatattctgtactaaggtttttttcaatataatctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
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gtattttccttccactt--tggaaatatctgctctcttaatcttcttacaactc-ttggattattacacatggcggcttgcatagttttctcatatttcatatctttcgaacactgacgacttatttactgt----tctgtagAATGCTCTGCGGCAACAAAGGTTTGTACGAGAAGTCACAATACAATACAATCTCTGCAATGAACCTTG
upper sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 7
gtaattttctacctcctctttctgttatcaatgttttcatttcaaagacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttgtctatattctgtactaaggtttttttcaatataatctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
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---------------------gtaatcacatggattttatt----aatcatgttagtattgttttatctattta---tttgttattataaatgataatcatct----tctttgatggtgttttgttc-----------ttcagAATGCGTTGCGGCAACAAAGATTTGTACGAGAAGTCACAATACAGTACAACTTATGTAATGAACCTTG
upper sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S55_201V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaattttctacctcctctttctgttatcaatgttttcatttcaaagacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttgtctatattctgtactaaggtttttttcaatataatctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
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---------------------------------tcgttgtatttatgtcactat-cagaaatttgtaactgatcgttaagtatctcaagtgctacattgttctttggtc---gtcaa----ttttgtaatgtgat--atgcagAATGCGTACCGGCAGCAAAGATTTATGCAGGAAGTGACAATACAGTACAATTTATGCAATGAACCGTGMapped 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|88327755|gb|CI657799.1|CI657799EST: TTGCTCCGGTTGCGGTTGAGCGCACAATGACAACAAGAGCAGCAGCTTCT AATGCGTTACGTC
genomic: TTGCTCCGGTTGCGGTTGAGCGCACAATGACAACAAGAGCAGCAGCTTCTgtaattttct ... atctatgcagAATGCGTTACGTC
EST:
gi|66917646|gb|CX104494.1|CX104494EST: TTGCTCCGGTTGCGGTTGAGCGCACAATGACAACAAGAGCAGCAGCTTCT AATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAAT
genomic: TTGCTCCGGTTGCGGTTGAGCGCACAATGACAACAAGAGCAGCAGCTTCTgtaattttct ... atctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAAT
EST:
gi|58689244|gb|CK077931.1|CK077931EST: TTGCTCCGGTTGCGGTTGAGCGCACAATGACAACAAGAGCAGCAGCTTCT AATGCGTTACGTCAACAAAGATTTG
genomic: TTGCTCCGGTTGCGGTTGAGCGCACAATGACAACAAGAGCAGCAGCTTCTgtaattttct ... atctatgcagAATGCGTTACGTCAACAAAGATTTG
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:
71 (upstream exon),
68 (downstream exon)
Score:
31TATTGATCTTGAGCCTCGCCTAAGCCATACATCAGCTGTGGAGCCTACACTTGCTCCGGTTGCGGTTGAGCGCACAATGACAACAAGAGCAGCAGCTTCTgtaattttct ... atctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagcaatctttgtctatattctgtactaaggtttttttcaatataatctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
tttttttcaatataat TA-rich tract