Sequence
atgc intronic sequence ATGC exonic sequenceGGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCCATGTGAGGGCAAGGAGAGGACAGGCAACTGATAGCCACAGCCTTGCAGAGAGGgtactactactgcacttcactttggttttggttttgatttttctgctgcttttgcatgagtggtttttggcttgcagcttctgcatcttttctcctggtctctgattcttggtgacattttctctctacag
Basic information
species | Oryza sativa |
transcript | LOC_Os08g42470.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g42470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G145579_T02 (Zea mays), 5'ss of exon 2
GGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCCATGTGAGGGCAAGGAGAGGACAGGCAACTGATAGCCACAGCCTTGCAGAGAGGgtac--tactactgcacttcactttggttttggttttgatttttctgctgcttttgcatgagtggtttttggcttgcagcttctgcatcttttctcctggtctctgattcttggtgacattttctctctacag
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GGAGAAGAGCAGCACTGATGAAGACGAGGCCTCCAAGGGGTACATCCATGTGAGGGCGAGGAGGGGCCAGGCGACAGACAGCCACAGCCTCGCAGAGAGGgtacgctgctgctaccactcgatctcatctacccccttctagtcttgcagcattaaacttgacagtt----agtcgtggtctcagtttctgctccccccgttc----tctttag-------------------
upper sequence: LOC_Os08g42470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G882527_T04 (Zea mays), 5'ss of exon 2
GGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCCATGTGAGGGCAAGGAGAGGACAGGCAACTGATAGCCACAGCCTTGCAGAGAGGgtactactactgcacttcactttggttttggtt---ttgatttttctgctgcttttgcatgag----tggtttttg-gcttgcagcttctgcatcttttc-tcctggtctctgattcttggtgac-attttctctctacag-----------------------------
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TGAGGAGAAGAGCGCTACTGAAGACGAGGCCACCAGGGGGTACATCCATGTGAGGGCGAGGAGGGGTCAGGCAACGGACAGCCACAGCCTTGCAGAGAGGgtac-agtac-acctctcactctaatccttgtagcattaatttgacagttagtcgtgtgtaatagtttggtctcagtacttcctgcctcccctctttttcgttatcttctcttgcatgaactgatgaacacctcccgatggcaattttttttgttggttggccttattag
upper sequence: LOC_Os08g42470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA04G37690.1 (Glycine max), 5'ss of exon 2
GGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCCATGTGAGGGCAAGGAGAGGACAGGCAACTGATAGCCACAGCCTTGCAGAGAGGgtactactactgcact-tcactttggttttgg----ttttgatttttctg-ctgcttttgcatgagtggttt-ttggcttgc---agcttctgcatcttt-tctcctggtctctgattcttggtgacattttctctctacag
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GAAGGAACAGAGAAAGTGTCCCGAAGAGCCTCCAACAGGCTATATCCATGTCAGAGCAAGAAGGGGTCAGGCAACGGATAGCCACAGCCTTGCTGAAAGGgtac-actgtaactctcttattaacaacttgaaaaattaccatctctatggctacgtgggccccaccagtgtgctggctttccctagaggtttcatcttcatgtttcattcctctaatgttgcaagaaaatggatttttcag
upper sequence: LOC_Os08g42470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA06G17420.1 (Glycine max), 5'ss of exon 2
GGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCCATGTGAGGGCAAGGAGAGGACAGGCAACTGATAGCCACAGCCTTGCAGAGAGGgtactactactgcacttcactttggttttggttttgatttttctg-----ctgcttttgcatgagtggttt-ttggcttgcagcttctgcatcttttctcctggtctctgattct--tggtg---------acattttctctctacag
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GAAGGATCAGAGAAAGTGTCCTGAAGAGCCCCCAACAGGCTATATCCACGTCAGAGCAAGAAGGGGTCAGGCAACGGATAGCCACAGCCTTGCTGAAAGGgtactgtactctcttaaaaactagaaaattattattatctctatgtatggctacgtggtccccaccagtgtgctggctttcc-ctagagtttttattatcttcatgtctcattctaatgttgcaagaaaatggattttcatttttcag
upper sequence: LOC_Os08g42470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv17s0000g00430.t01 (Vitis vinifera), 5'ss of exon 2
---GGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCCATGTGAGGGCAAGGAGAGGACAGGCAACTGATAGCCACAGCCTTGCAGAGAGGgtactact----actgcacttcactttgg------ttttggttttgatttttctgctgcttttgcatgagtggtt-tttggcttgcagcttctgcatcttttctcctggtctctgat-tcttggtgacatt-----ttctctctacag----------------------------------------------------
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GAAGGATCAGAAGAAAGCCTCTGAAGA---GCCTCCAACCGGCTACATTCATGTAAGAGCAAGGAGGGGCCAAGCAACAGACAGCCACAGCCTTGCAGAGAGGgtactactgttcactaatattaattattaaaagcccatggaacccagtgtctttgttacatttattaaggcattagtttcccataataccccaacaacaaatcacagagttttcaatgttttggtacctaccagaatagtttctaaaagaatttctcaccctattcttacaactattcattttcttcaaatgggttccagMapped 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|163926679|gb|EG713695.1|EG713695EST: TGAGGGCAAGGAGAGGACAGGCAACTGATAGCCACAGCCTTGCAGAGAGG GTGAGGAGGGAGAGGATCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTC
genomic: TGAGGGCAAGGAGAGGACAGGCAACTGATAGCCACAGCCTTGCAGAGAGGgtactactac ... ctctctacagGTGAGGAGGGAGAGGATCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCCATGTGAGGGCAAGGAGAGGACAGGCAACTGATAGCCACAGCCTTGCAGAGAGGgtactactactgcacttcactttggttttggttttgatttttctgctgcttttgcatgagtggtttttggcttgcagcttctgcatcttttctcctggtctctgattcttggtgacattttctctctacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG