Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcctgtgtatattttgttgtttcaatatgattgtagattgttttagtgcccttttatcctgtgcatgctctaggctatgtagttttttggttaatggtagtaaaaggttaatagcaatgatttaccaatgagtactatttcatatttggaaggtatttcaactattacttttatttttatcctacagGACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g40820.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 2
gtaagttcctgtgtatatt-ttgttgtttcaatatgattgtagattgtt--ttagtgcccttttatcctgtgcatgctctaggctatgtagttttttggttaatggtagtaaaaggttaatagcaatgatttaccaatgagtactatttcatatttggaaggtatttcaactattacttttatttttatcctacagGACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG
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gtaagtttctgcatcttttattgcaattgaaatattattagatctggttagtcaatgcc-tttccttttctgcatgat-taggatat---tttatgtgactgat--taatgactattcta-agaaatg--ttattagcaagagttactg---atctcaaaattgttctaagtatga-tcatatccttg-----cagGACAGAACTCTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCATCCGATTTATCCGTGCTGATTCTCAG
upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G142640_T03 (Zea mays), 3'ss of exon 1
gtaagttcctgtgtatatt-ttgttgtttcaatatgattgtagattgttttagt----gcccttttatcctgtgcatgctctaggctatgtagttttttggttaatggtagtaaaaggttaatagcaatgatttaccaatgagtactatttcatatttggaaggtatttcaactattacttttatttttatcctacagGACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG
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gtaagtttctacttcttttattgcaattgaaatatgttaatagatctggttagtctatgactctatgtccttatttttctgcatggctaatgtattttctgtgattgattaataattgtcga-actaatg--ttattagaaagagttat---ggatcgtgaagttattctaag---tacattcatctc---cttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCATTAGATTTATCCGTGCTGATTCTCAG
upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G074898_T03 (Zea mays), 3'ss of exon 2
gtaagttcctgtgtatattttgttgtttcaatatgattgtagattgttttagtgc---ccttttatcctgtgcatgctctaggctatgtagttttttggttaatggtagtaaaaggttaatagcaatgatttaccaatgagtactatttcatatttggaaggtatttcaactattacttttatttttatcctacagGACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG
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gtaagtttctatttcttttctttcatttaaatatgttaaaatatctggctagaccatgcctttttttctcggcatg------acta-gcatattttctgtgattggtt----aatgttattagaaacagtta-----------------cacatcttgaaattattctaagtacga---tcatct---ccttgcagGACGGAACTCTGCCGCTTCAGTGGCCAGAAGATCTATCCTGGGAAAGGCATCCGGTTTATTCGTGCTGATTCTCAGMapped 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|88397656|gb|CI684589.1|CI684589EST: AATTCTGTGAGTATTTAAGCTGAGAAGATGGTGCTGAA GACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAAGGGCA
genomic: AATTCTGTGAGGATTTAAGCTGAGAAGATGGTGCTGAAgtaagttcct ... tatcctacagGACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGG-AAGGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactatttcatatttggaaggtatttcaactattacttttatttttatcctacagGACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG
cttttatttttatcct CT-rich tract
tatttcaactattact TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcctgtgtatattttgttgtttcaatatgattgtagattgttttagtgcccttttatcctgtgcatgctctaggctatgtagttttttggttaatggtagtaaaaggttaatagcaatgatttaccaatgagtactatttcatatttggaaggtatttcaactattacttttatttttatcctacagGACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG
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