Sequence
atgc intronic sequence ATGC exonic sequenceGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggatgttctgctttgcattttgatagtctttattttctgaagaccgtttggaaattagtattatattttccttacattattaaccccttgttgtgtaaataatttatctgtag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g30540.1 |
intron # | 26 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 26
GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggatgttctgctttgcattttgat---------agtctttattttctgaagaccg-------------------tttg-gaaattagtattatattttccttacattattaaccccttgttgtgtaaataatt--tatctgtag
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GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcatgatttatgtgaagtatttaccgaatgaagagtcctggctctttctaatccaatgttctagaatttctgaatttgtaaaattagtgttatttttttccttaaacttggcattgttagtatg-atataattattttctgcag
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 16
GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggatgttctgcttt--gcattt------tgatagtcttta---ttttctga-----------agaccgtttgga-------aattagtattatattttccttacattattaaccccttgttgtgtaaataatt--tatctgtag
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GTTGAACTATCTAATCCTGACGCTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgttcgtgcatggtttatctgaagtatttcctgcatgaaaggtcctggctttttctaatgcaatattctagaatttctgaacttctaaaattagtgttatattttcccttaaatttgacattgttaggatg-atataattattttctgcag
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA13G16040.1 (Glycine max), 5'ss of exon 7
GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtcc----ttggatgttctgctttgcattttgatagtctttattttctgaagaccgtttggaaa---ttagtattatattttccttacattattaaccccttgttgtgtaaataatttatctgtag
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GTAGAGTTATCTGATCCTGAAGCTGAACTTCGGTTGCTTGAAGTCTTCTATCACAAAATATACAAGgtatgaaattacatgtgttgatg-acttgtggatgtattactctattttgttattgtttaaaaaaaatcaactggaaatcttgattaaattttcaatttca-------------------------
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA10G23680.1 (Glycine max), 5'ss of exon 22
GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggatgttctgctttgcattttgatagtctttattttctgaagaccgtttggaa--attagtattatattttccttacattattaaccccttgttgtgtaaataatttatctgtag
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GTAGATCTATCACATCCTGATGCAGAACTTAGATTGCTTGAAGTTTTCTATCACAAGATTTATAAGgtg--tggagaatatagttt----tttaat----ctcactttcagatactcgtattatcctattagtagtgaaaatgatttcccttg----ctcttcatgaggtgaaaagtgaa-------
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA20G11330.1 (Glycine max), 5'ss of exon 18
GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggatgttctgctt--tgcattttgatagtctt--tattttctgaagaccgtttggaaattagtattatattttccttacattattaaccccttgttgtgtaaataatttatctgtag
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GTAGAGTTATCTGATCCTGAAGCTGAACTTCGGTTGCTTGAAGTCTTCTATCACAAAATATACAAGgtatgaaattacacgcgttgatgacttgtggatgtattactatattttgttattgtttaaaaaagaaatcatctgggaatcttg-atta--aatttactattc--------------------
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 26
GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggatgttctgctttgcattttgatagt-ctttattttctgaagaccgtttggaaattagtattatattttccttacattattaaccccttgttgtgtaaataatttatctgtag
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GTTGAGCTGTCTCATCCTAATGCTGAAGTTAGGTTGCTTGAAGTTTTCTATCACAAGATCTATAAGgtgt---aagctttatctttgcatgctattactactctggttgatgatgatcgttt-----ctggaagaaaaatatcataagaccat-actccttttctgggt---ttattt--------
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 26
GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggatgttctgctttgcattttgatagtctttattttctgaagaccgtttggaaattagtattatattttccttacattattaaccccttgttgtgtaaataatttatctgtag
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GTTGAGTTGTCTCATCCAAATGCAGAACTTAGACTGCTTGAAGTTTTCTATCACAAGATTTATAAGgtaat--ggctttatgattggacttgaagttctaccaatataatagtgttctttttctgctaaacac-agactcttttgac-ttgtca-ctctttgtggagttga--------------
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 26
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 5'ss of exon 26
GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtcc-ttgga---tgttctgctttgcatt-ttgatagtctttattttctgaagaccgtttggaaattagtattatattttccttacattattaaccccttgttgtgtaa-----ataatttatctgtag-------------------------------------------------------------
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GTTGAACTTTCGAGTCCAAGAGCAGAGCTTCGCATTCTTGAAGTATTCTATCACAAAATTTATAAGgtttgctacaacttgttttcttttatgggattggtaatttagattgacc-aatcctaggtgaaattttgaacctaatgaaattctcaatattaggatattgtatagtactattcgagatttcttgatagtgtttttagacataatcaatagcatttaatagttttctgtgtaataatttgtctttttcagMapped 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|25799966|gb|CA755927.1|CA755927EST: CTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG ATATTTCCACCTCACGAGAAAATAGAGAACATTAATGATCAGTACTGGA
genomic: CTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggat ... ttatctgtagATATTTCCACCTCACGAGAAAATAGAGAACATAAATGATCAGTACTGGA
EST:
gi|58678315|gb|CK067002.1|CK067002EST: CTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG ATATTTCCACCTCACGAGAAAATAGAGAACATAAATGATCAGTACTGGACA
genomic: CTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggat ... ttatctgtagATATTTCCACCTCACGAGAAAATAGAGAACATAAATGATCAGTACTGGACA
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:
66 (upstream exon),
66 (downstream exon)
Score:
79GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggat ... ttatctgtagATATTTCCACCTCACGAGAAAATAGAGAACATAAATGATCAGTACTGGACACTACGTGCTGAGGAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAGgtccttggatgttctgctttgcattttgatagtctttattttctgaagaccgtttggaaattagtattatattttccttacattattaaccccttgttgtgtaaataatttatctgtag
- - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - TTGAAG