Sequence
atgc intronic sequence ATGC exonic sequenceTCGAGTTGCTGGATGGATCGAGTTGTTTCAAGCTCTACATCAATGCTTGGACAGTAATGATCTGGATCATATGGAAGGTGCTATGGATGCTATATACAAGgtaaacttctctctcatatttttgagcctgatctgtgattttcacatagaagacttcgaacagttggtgtctacgtgcttaagcagtaactcagtagcgaacctgtagcatgaatactctatgtgaacttgaacatgatttgcatgctcaaaaacttgtttttctacag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g59494.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g59494.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 2
TCGAGTTGCTGGATGGATCGAGTTGTTTCAAGCTCTACATCAATGCTTGGACAGTAATGATCTGGATCATATGGAAGGTGCTATGGATGCTATATACAAGgtaaacttctctctcatatttttgagcctgatctgtgattttcacatagaagacttcgaacagttggtg-tctacgtgcttaagcagtaactcagtagcgaacctgtagcatgaatactctatgtgaacttgaacatgatttgcatgctcaaaaacttgtttttctacag
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ACGAGTCGCTGGATGGATTGAGTTGTTTCAGGCACTCCATAAGTGTTTGGAGAGTAATGACCTGGATCACATGGAAGGTGCTATGGATGCGATATACAAGgtaatgtgcacttctgtcatactaggggt--tccatgcattaaaccagcatgatgtagtatatcttacaatttgcgttctcaaagtcttgctttccgatgacag------------------------------------------------------------------
upper sequence: LOC_Os04g59494.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G312026_T01 (Zea mays), 5'ss of exon 2
TCGAGTTGCTGGATGGATCGAGTTGTTTCAAGCTCTACATCAATGCTTGGACAGTAATGATCTGGATCATATGGAAGGTGCTATGGATGCTATATACAAGgtaaacttctctctcatatttttgagcctgatctgtgattttcacatagaagacttcgaacagttggtg-tctacgtgcttaagcagtaactcagtagcgaacctgtagcatgaatactctatgtgaacttgaacatgatttgcatgctcaaaaacttgtttttctacag
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ACGAGTTGCTGGATGGATTGAGTTGTTTCAGGCACTCCATAAGTGTTTGGAGAGTAATGACCTGGATCACATGGAAGGTGCTATGGATGCGATATACAAGgtaatgtacactcctgtcatactaggggt--tccatgcattaaaccagtatggtgtaatgtatcttacaatttgctttttcaaaatgttgctttctgatgacag------------------------------------------------------------------
upper sequence: LOC_Os04g59494.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G42960.1 (Glycine max), 5'ss of exon 2
TCGAGTTGCTGGATGGATCGAGTTGTTTCAAGCTCTACATCAATGCTTGGACAGTAATGATCTGGATCATATGGAAGGTGCTATGGATGCTATATACAAGgtaaacttctctctcatatttttgagcctgatctgtgattttcacatagaagacttcgaacagttggtgtctacgtgcttaagcagtaactcagtagcgaacctgtagcatgaatactctatgtgaacttgaacatgatttgcatgctcaaaaacttgtttttctacag
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AGGAGTTGTTGGGTGGCCTGAATTGTTGCAAGCCCTCGTAAGTTGCTTGGATAGTAATGATCTAAATCACATGGAAGGTGCTATGGATGCGTTATCCAAGgtatggtctcc------attttagag-----tcaataatgttcttaaattgtagttc---tggctaaaatcaa-atcttcaa--agaaaatgaa-agtactttcattatatggattgg---------------------------------------------------
upper sequence: LOC_Os04g59494.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G24040.1 (Glycine max), 5'ss of exon 2
TCGAGTTGCTGGATGGATCGAGTTGTTTCAAGCTCTACATCAATGCTTGGACAGTAATGATCTGGATCATATGGAAGGTGCTATGGATGCTATATACAAGgtaaacttctctctcatatttttgagcctgatctgtgattttcacatagaagacttcgaacagttggtgtctacgtgcttaagcagtaactcagtagcgaacctgtagcatgaatactctatgtgaacttgaacatgatttgcatgctcaaaaacttgtttttctacag
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AGGAGTTGTTGGGTGGCCTGAATTGTTGCAAGCCCTTGTAAATTGCTTGGATAGTAATGATCTAAATCACATGGAAGGTGCAATGGATGCGTTATCTAAGgtatgttctcc------attttagagtcaa---taatgtttttaaattgtagttct-----ggctaaaatcaa-atcttcaa--agaaaatgaa-agtactttcattatatggattgg---------------------------------------------------
upper sequence: LOC_Os04g59494.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 5'ss of exon 2
TCGAGTTGCTGGATGGATCGAGTTGTTTCAAGCTCTACATCAATGCTTGGACAGTAATGATCTGGATCATATGGAAGGTGCTATGGATGCTATATACAAGgtaaacttctctctcatatttttgagcctgatctgtgattttcacatagaagacttcgaacagttggtgtctacgtgcttaagcagtaactcagtagcgaacctgtagcatgaatactctatgtgaacttgaacatgatttgcatgctcaaaaacttgtttttctacag
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GGGAGTTTCTGGATGGCCTGAGCTCTTGCAAACTCTTGCTAATTGCTTGGAAAGTAATGACTTAAATCATATGGAAGGTGCTATGGATGCTTTGTCTAAGgtaggtcccacttttacattgatg-gtttgttctat--tcttcgtttctga---tctaaagaat--gcattta-gtgattgtg-atgaactgaat-gcatagtggtggtgt----------------------------------------------------------Mapped 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|29627775|gb|CB632786.1|CB632786EST: ACAGTAATGATCTGGATCATATGGAAGGTGCTATGGATGCTATATACAAG ATCTGTGAGGATGTTCCTGAGGAGCTTGATGTTGATGTTCCTGGTTTGCCT
genomic: ACAGTAATGATCTGGATCATATGGAAGGTGCTATGGATGCTATATACAAGgtaaacttct ... ttttctacagATCTGTGAGGATGTTCCTGAGGAGCTTGATGTTGATGTTCCTGGTTTGCCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCGAGTTGCTGGATGGATCGAGTTGTTTCAAGCTCTACATCAATGCTTGGACAGTAATGATCTGGATCATATGGAAGGTGCTATGGATGCTATATACAAGgtaaacttctctctcatatttttgagcctgatctgtgattttcacatagaagacttcgaacagttggtgtctacgtgcttaagcagtaactcagtagcgaacctgtagcatgaatactctatgtgaacttgaacatgatttgcatgctcaaaaacttgtttttctacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG