Sequence
atgc intronic sequence ATGC exonic sequencegtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaattgttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g48650.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G099452_T02 (Zea mays), 3'ss of exon 4
gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaattgttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
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----------------------------------------------------------------caagatgcctggcctgcaagatca-ttctgcttgtttctcttgttttttgggatagcaacaagacttatttggtgcatgtat-----ggtctttttccttcaacagCCACACAGCTGCAATTGCTGCTGGAAACAATGGGATTCCGGTGCGAATGCATGGTCACGAGTTTGGCAAAGCAAGTGGCATGGCCCCACGTGCTAG
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G114394_T02 (Zea mays), 3'ss of exon 4
gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaattgttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatg--ctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
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-----------------------------------------------------------tcctgatgcctggcctg--caaaa------ttattctggttgtttcttttgttttctggga--acataacaaaac---ttatctgatgcatgtatggtcttttccttcaacagTCACACAGCTGCAATTGCTGCTGGAAACAATGGGGTCCCAGTGCGAATGCATGGTCACGAATTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAG
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 3
gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaattgttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
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-----------------------------------------------------------------ctatttctatgtcttataaacataggaaatgggtagta--ccaatttgataacgattgt-tcttttaac-aattccccgttgttcttgcatcttcatctgg-cagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 3
gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaattgttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
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----------------------------------------------------------------atagttttagcactcgctgcatca-ttcttaaagacacatatctttt-----aatttgataacatttttttaacaatcctctgttttcatgcatcatctctggcagTCATACAGCCTCTATTGCGGCTGGAAATAATGGAATTCCTGTGAGAATGCATGGCCACGAATTTGGGAGAGCGAGTGGGATGGCTCCTCGTGCTAG
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 4
----------------------gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatac---------atgaaaattgttc---tgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
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gttagaccatgcttccttctttattaacttcttcacttggaagtaggattcttcagatgctctctttataaggggtgctgtgctcaaaataaaagaaaactgtttctatgtcttataaacataggaaatgggtagta--ccaatttgataacggttgttctgttaac--aattcccccattcttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaattgttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
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------------------------------------------------------------------------------------gtttgtctttaaagttgtctccaggtgttaggggga-gataatgctgttgtactaagcaaatctgattatgctggatttt---cagTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 4
gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaatt--gttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
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-------------------------------------------------------------atgatagtttgattttcttttaatattt---tgttcccatt-tactctgttttatttgattgggtctggttcattt-gttgttt--cttgggaatactggac----aacagTCACACAGCAGCTATTGCAGCTGGAAATAATGGAATTCCAGTGAGAATGCATGGGTATGAATTTGGGAAAGCAAGTGGGATGGCTCCCCGTGCCAGMapped 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|88720601|gb|CI743900.1|CI743900EST: AATCCTGATGTCGATTTTGCATCTCCATTAGATGGCGATGGCCATGGAAG TCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCA
genomic: AATCCTGATGTCGATTTTGCATCTCCATTAGATGGCGATGGCCATGGAAGgtcatgctcc ... ccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCA
EST:
gi|58681743|gb|CK070430.1|CK070430EST: AATCCTGATGTCGATTTTGCATCTCCATTAGATGGCGATGGCCATGGAAG TCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCA
genomic: AATCCTGATGTCGATTTTGCATCTCCATTAGATGGCGATGGCCATGGAAGgtcatgctcc ... ccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCA
EST:
gi|58607175|gb|CK035208.1|CK035208EST: AATCCTGATGTCGATTTTGCATCTCCATTAGATGGCGCTGGCCATGGAAG TCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCC
genomic: AATCCTGATGTCGATTTTGCATCTCCATTAGATGGCGATGGCCATGGAAGgtcatgctcc ... ccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
atctgat putative branch site (score: 4)
tgctttccctt putative PPT
ttatcta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaattgttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG