Sequence
atgc intronic sequence ATGC exonic sequenceGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgagaatttttttgccttaggcacttaaatctctattttccatcttctaacctccctaacaaaaaccatgtcattacaaatatatcttgtgtggattat...
Basic information
species | Oryza sativa |
transcript | LOC_Os07g30840.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G085670_T03 (Zea mays), 5'ss of exon 4
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgag-------aatttttttgccttaggcacttaa-atctctattttccat--cttctaacctccctaacaaaaaccatgtcattacaaatatatcttgtgtggattat-----------------------------------------------------------------------------------------
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ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgttacatcctctttaaattagatacttaatatttgcataaaccattcctgtgagactcgtaaatgcgtcatttaccactaatggtagtattttttcttcttatttttagtggttttacattggtctttagtttctagtgttgcctaaagtatttttggcgtcatatccataatattatgcatgttcatgtag
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G171745_T05 (Zea mays), 5'ss of exon 3
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgaga-atttttttgccttaggcacttaaatctc-tattttccatcttctaacc--tccctaacaaaaaccatgtcattacaaatatatcttgtgtggattat------------------------
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ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgttacatcctctttaaattttggctctggtatttttcttattttcagtggtttttaatacttctagtgttgcctaaagtatttttgacatcatatccataatattctgcatgttcatgcag
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G152805_T01 (Zea mays), 5'ss of exon 4
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgag-------aatttttttgccttaggcacttaa-atctctattttccat--cttctaacctccctaacaaaaaccatgtcattacaaatatatcttgtgtggattat-----------------------------------------------------------------------------------------
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ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgttacatcctctttaaattagatacttaatatttgtataaactattcctgtgagacttgtaaatgtgtcatttaccactaatggtagtattttttcttcttatttttagtggttttacattggtctttagtatctagtgttgcctaaagtatttttggcatcatatccataatattatgcatgttcatgtag
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G085670_T06 (Zea mays), 5'ss of exon 4
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgagaatttttttgccttaggcacttaaatctctat-tttccatcttctaacctccctaacaaaaaccatgtcattacaaatatatcttgtgtggattat
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ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACgtaagagaactcgaagattttctaatcaatgagtgcatgtattcagtgagttgttacatcctctttaaattagatacttaatatttgcataaaccattcc----------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G152100_T02 (Zea mays), 5'ss of exon 2
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG-
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ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATGCAagagttggatgtttccaacgtaagagaactcgaagattatgcatgttcatgtag-------------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G152100_T02 (Zea mays), 5'ss of exon 2
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG-
| |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| || ||||||||||||||||| | || || ||| | | || | | | ||| || | ||
ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATGCAagagttggatgtttccaacgtaagagaactcgaagattatgcatgttcatgtag-------------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G115277_T02 (Zea mays), 5'ss of exon 4
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgag-------aatttttttgccttaggcacttaa-atctctattttccatcttct--aacctccctaacaaaaaccatgtcattacaaatatatcttgtgtggattat-----------------------------------------------------------------------------------------
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ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgttacatcctctttaaattagatacttaatatttgtataaaccattcttgtgagactcgtaaatgtgtcatttaccactaatggtagtattttttcttcttatttttagtggttttacattggtctttagtatctagtgttgcttaaagtatttttggtatcatatccataatattatgcatgttcatgtag
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G027551_T01 (Zea mays), 5'ss of exon 2
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG-
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ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATGCAagagttggatgtttccaacgtaagagaacttgaagattatgcatgttcatgtag-------------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G027551_T01 (Zea mays), 5'ss of exon 2
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG-
| |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| || ||||||||||||||||| | || || ||| | | || | | | ||| || | ||
ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATGCAagagttggatgtttccaacgtaagagaacttgaagattatgcatgttcatgtag-------------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv15s0021g01580.t01 (Vitis vinifera), 5'ss of exon 4
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgagaatttttttgccttaggcacttaaatctctatttt-ccatcttctaacctccctaacaaaaaccatgtcattacaaatatatc-ttgtgtggattat------
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GTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCGgtaggtatt------catcaagc--tggattctgcatccaaccaaactatagactgttttgagaaattcttgtaatgctaggaaaataattattttaactgtcccagg
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv02s0234g00120.t01 (Vitis vinifera), 5'ss of exon 4
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgagaatttttttgccttaggcacttaaatctctattttccatcttctaacctccctaacaaaaaccatgtcattacaaatatatcttgtgtggattat---
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GTTCTCTCCTACTATCAACTGATGCAGGAACTTGATATTTCTAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATCAATGCGgtgggt-cctcttggttttgacaagttttatgaattctcctaaatagtgaattataatacctgcag--attttgaaggaacttggcattttatgatcccttctMapped 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|86499691|gb|CI142324.1|CI142324EST: CCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG GGTATTGTCAGGGCCAAATTGGATCAGCTCCGGAGGTGTTTTGAG
genomic: CCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgagaattt ... gcttccctagGGTATTGTCAGGGGCAAATTGGATCAGCTGCGGAGGTGTTTTGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCGgtgagaatttttttgccttaggcacttaaatctctattttccatcttctaacctccctaacaaaaaccatgtcattacaaatatatcttgtgtggattat
- - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA