Sequence
atgc intronic sequence ATGC exonic sequenceGCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacacaatatctccatttatgttgattgttatattgaaccttttatggcttctacagatataatgttatcatctctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52900.1 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G084181_T01 (Zea mays), 5'ss of exon 17
GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacacaatatctccatttatgttgattgttatattgaaccttttatggcttctacagatataatgttatcatctctgcag
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GCTTGGAGAAATACCACCAGTATCTGGATCAGGTACCTCAGTGGTCATTCGTGGATCGGTGGCTTACGTTCCTCAAGTTTCCTGGATCTTCAATGCTACTgtgagattc----tctgctgctttgttg--tgttaaatcaaaccctatataacttctgcagagatctaactgtga-ccccacag
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA15G09900.1 (Glycine max), 5'ss of exon 17
------GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagaca-caatatctccatttatgttgattgttatattgaaccttttatggcttctacagatataatgttatcatctctgcag--------------------
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TGCAATGCTTGGAGAACTTCCACCAATGGCAG------ATTCATCTGTTGTTTTGAGAGGAACAGTTGCTTATGTACCCCAAGTTTCCTGGATTTTTAATGCAACTgtaagttaataatatattctattaagaaaagt-tcata----actttttacaaccgggagaaagaggataagaaaatgctgagagataaataagttggaaagtaa
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA13G29180.1 (Glycine max), 5'ss of exon 17
------GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagaca-caatat-ctccatttatgttgattgttatattgaaccttttatggcttctacagatataatgttatcatctctgcag---------------
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TGCAATGCTTGGAGAACTTCCTCCGATGGCAGATTCAACT------GTTGTTTTGAGAGGAACAGTTGCTTATGTACCCCAAGTTTCATGGATTTTTAATGCAACTgtaagttaataatatattctatttagaatagataataactttatacaattg-ggagaacaaagataagaagatcttgagagagaaataagttggaaagtaa
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 17
lower sequence: AT1G30400.2 (Arabidopsis thaliana), 5'ss of exon 17
------GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacacaatat----ctccatttatgtt--gattgttatattgaaccttttatggcttctacagatataatgttatcatctctgcag------------------------------------------------------------------------------
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TGCTATGCTTGGGGAACTTCC-----TG-CAAGATCTGATGCGACTGTTACTCTTAGAGGATCAGTCGCTTATGTTCCACAAGTTTCATGGATCTTTAACGCAACAgtaagtttatatatgctactcagtttatagtatggttctcaatgcgaaaatgtca--aattctcctcttggattgttacttattttgtatgtattttatgttttgtatatgatgatgtgtgcttttagatacgtccacatgctgatggttgtaattaacatcgcgtag
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 17
lower sequence: AT1G30410.1 (Arabidopsis thaliana), 5'ss of exon 19
------GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacaca-atatctcc-atttatgttgattgt------tatattgaaccttttatggcttctacagatataatgtta-tcatctctgcag------------------------------------------
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GGCAATGCTGGGGGAGTTATCTC--ATGCTGAAACC----ACAAGCGTTGTTATTAGAGGCTCTGTAGCTTATGTTCCTCAAGTTTCGTGGATCTTCAATGCCACTgtgagtcgcctatacttcctgcttgctctgaaaacaaaaactattttatagctttaagtacctttattttcatttggtcaattagttaggcacttaggctggaagtgtcccaatacaagtgcctatgtattgcag
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 17
lower sequence: AT2G34660.1 (Arabidopsis thaliana), 5'ss of exon 17
------GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacacaatatctccatttatgttgattgttatattgaaccttttatggcttctacag-atataatgttat-catctctgcag-----------------
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TGCTATCCTTGGTGAACTTCCTGCAACATCTG------ATGCAATAGTTACTCTCAGAGGATCAGTTGCTTATGTTCCACAAGTTTCATGGATCTTTAATGCAACAgtatgttct--tcttttctttgacttttaa-gttgggctgacgttgcaaatttttctgttgtacataatgttaaatgtattttctgtcttttatagtagaaca
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 17
lower sequence: AT1G30420.1 (Arabidopsis thaliana), 5'ss of exon 17
------GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacacaatatctccatttatgttgattgttatattgaaccttttatggcttctacagatataatgttatcatctctgcag-----------------------------------------------
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GGCAATGCTGGGGGAGTTATCTC--ATGCTGAAACCTCAAGCGTTGATA----TCAGAGGATCTGTAGCTTATGTACCTCAAGTTTCATGGATCTTTAATGCCACTgtgagtcccctttacttc-ttgctggctctgaaaacattaactgtattataacttttt--ggtagcttttttttaattcggtcaattagttaggcaggaagcgtcctaatacaagtgtctatgcattgcag
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 5'ss of exon 18
------GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacacaatatctccatttatgttgattgttatattgaaccttttatggcttctacagatat----aatgttatcatctctgcag----------------------------------------------------------
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AGCAATGCTTGGGGAGCTGCCTCCTTTGTCAGATGCAAGT------GTTGTTATCAGAGGGACTGTTGCATATGTTCCTCAAATTTCATGGATTTTCAATGCCACTgtaagtttcagcatgcttggattctcttatggtatcagatatcttagctaagcagctgccagtgtttacaacactctgggccttgcagtattttattcatttccaattcactgcaaaatgcggaccttgaatgcttattaatacag
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 5'ss of exon 17
------GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacacaatatctccatt-tatgttgattgttatattgaacctttt-atggcttctacagatataatgttatcatctctgcag--------------
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GGCAATGCTGGGGGAGCTGCCTCCAATGTCAGATGCAAGT------GCTGTTATAAGAGGAACAGTTGCTTATGTTCCACAAGTTTCATGGATTTTCAATGCCACTgtgagtttcagcatatttgttctgcattactatctatttcttgtctaatgatcaggggcttacaaccaatcttcccatccttggtgatggaagcatgctg
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv10s0003g04450.t01 (Vitis vinifera), 5'ss of exon 6
------GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacacaatatctccatttatgttgattgttatattgaaccttttatggcttctacagatat-----aatgttatcatctct-gcag------------------------------------------------------------
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AGCAATGCTTGGGGAGCTGCCTCCTGCAGCAGATGCAAGT------GTTGTTATTAGAGGGGCTGTTGCTTATGTTCCTGAAGTTTCATGGATTTTCAATGCCACTgtgagttgctggatgcttgtattctttggtt-ctgttgcatagcttagctagatactggccatattttggaacattagtggatcttatagtgaatctcatccattttttaccaattgcacatcgctgaccttcaaagtttgtccttacagMapped 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|157650622|gb|EX450256.1|EX450256EST: GTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACT GTCCGGGACAATATATTGTTTGGGTCTCCCTTCCAACCTCCACGCTACGAG
genomic: GTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacaca ... atctctgcagGTCCGGGACAATATATTGTTTGGGTCTCCCTTCCAACCTCCACGCTACGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTTGGTGAAATACCACCAGTGTCAGGATCGAATACATCGGTGGTCCTTCGTGGAACAGTGGCTTATGTTCCTCAAGTTTCATGGATCTTCAATGCAACTgtgagacacaatatctccatttatgttgattgttatattgaaccttttatggcttctacagatataatgttatcatctctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA