Sequence
atgc intronic sequence ATGC exonic sequence...ctttgttaggcatggattctcttagattatttgacttccttccttttaaagactaggcatgacacgtttctctacgccattaacatattcacctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g15040.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 6
-ctttgttaggcatggattctcttagattatttgacttccttccttttaaagactag-gcatgacacgtttctcta-cgccattaacatattcacctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT
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tgaatatcagaactataaccattacttttgcatga--tgcattttttcatgaactaatacatttaattttccattaatatcattgtcatgtgtgcatttc-agGCCATACTGGCGGTGCTACTTTCCAAACACCCAGGCTATCATATATGTTGTTGATTCAAGCGATACAGATAGGCTTGTAACAGCAAAAGAAGAATTCCAT
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G07390.1 (Glycine max), 3'ss of exon 4
ctttgttaggcatggattctcttagattatttgacttcct-tccttttaaagactaggcatgacacgtttctctacgccattaacatattcacctttt-----tagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT
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------acactttgtattgcctttatatatgttatacattatagatgtaatgtccatttatttctcccacttttttttggtttgattttttactttttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACCCAAGCAATAATCTATGTTGTTGATTCAAGTGACGTTGATAGGCTTGTGATAGCTAAGGAGGAGTTCCAT
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G01270.1 (Glycine max), 3'ss of exon 4
--ctttgt-taggcatggattctcttagattatttgacttccttccttttaaagactaggcatgacacgtttctctacgccattaacatattcacctttt-----tagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT
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cactttgtattaccattatgtgttatagattatc-gatgtaatgtc------aatttatttctcccacttttttttgtttgattgtt-tttttactttttgtccatagGCCATATTGGAGGTGTTACTTTCCAAATACTCAAGCAATAATCTATGTTGTTGATTCAAGTGACGTTGATAGGCTTGTGATAGCTAAGGAGGAGTTCCAT
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0052g01720.t01 (Vitis vinifera), 3'ss of exon 5
--ctttgttaggcatggattctcttag--attatttgacttccttccttttaaagactaggcatgacacgtttctctacgccattaacatattcacctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT
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caatgtttcaatttacctttcttttgggcataatttg--taagtttgcatcaagggcacaggatcatcagctgct-tgtttggtttatgt-tttttgggcacagGCCATATTGGAGATGCTATTTTCCAAATACTCAAGCCATAATATATGTTGTTGATTCAAGTGATACTGATAGATTGGTAATAGCTAAAGATGAGTTTCAT
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0008g07360.t01 (Vitis vinifera), 3'ss of exon 4
ctttgttaggcatggattctcttagattatttgacttccttccttttaaagactaggcatgacacgtttctctacgccattaacatattcaccttttta--gGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT
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--ctgttgttctgtgaagcttatagattattatgctgattgctttaaggttattatctctgcaattcattggctcatcaactgtttcttcattttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGTTGACTCAAGTGACACTGATAGAATTGTAATAGCCAAGGATGAATTTCAT
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ37645 (Selaginella moellendorffii), 3'ss of exon 4
ctttgttaggcatggattctcttagattatttgacttccttccttttaaagactaggcatgacacgtttctctacgccattaacatattcacctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT
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-----------gtgagtgatcgcgg-tcattt--tttcttttgtttcaaacactttg--------gtttgctgac-----------actcatcattc-agACCTTACTGGAGATGCTACTTTCCAAACACACAGGCTGTGATTTACGTTGTTGATTCGACTGACACGGAAAGAATGGCAACTGCAAAGGACGAACTCCAC
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ14920 (Selaginella moellendorffii), 3'ss of exon 4
ctttgttaggcatggattctcttagattatttgacttccttccttttaaagactaggcatgacacgtttctctacgccattaacatattcacctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT
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------------------------------gtgagtatcttttgtttcaa-----------acactttggtttgc-----tgaca--ctcatcattc-agACCTTACTGGAGATGCTACTTTCCAAACACACAGGCTGTGATTTACGTTGTTGATTCGACTGACACGGAAAGAATGGCAACTGCAAAGGACGAACTCCACMapped 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|88383993|gb|CI631883.1|CI631883EST: ATCTCGGTGGTCAAACAAGCATCAG GCCATACTGGAGATGCTACTTTCCAACATACC-AGGCTATCATTTATGTTG
genomic: ATCTCGGTGGTCAAACAAGCATCAGgtaccatctc ... acctttttagGCCATACTGGAGATGCTACTTTCCAA-ATACCCAGGCTATCATTTATGTTG
EST:
gi|27554607|gb|CA998507.1|CA998507EST: ATCTCGGTGGTCAAACAAGCATCAA GCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
genomic: ATCTCGGTGGTCAAACAAGCATCAGgtaccatctc ... acctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaagactaggcatgacacgtttctctacgccattaacatattcacctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT
cattaac putative branch site (score: 2)
ttcaccttttt putative PPT
attaacatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttgttaggcatggattctcttagattatttgacttccttccttttaaagactaggcatgacacgtttctctacgccattaacatattcacctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG