Sequence
atgc intronic sequence ATGC exonic sequence...gtgcaattgtgatacctacaaatattgttttgatgctgcctatttaaaatgttaaatgatggcattctttttttttttcacatgctctgttcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52370.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G044629_T03 (Zea mays), 3'ss of exon 6
gtgcaattgtgatacctacaaatattgttttgatgctgcctatttaaaa-----tgttaaatgatggcattctttttttttttcacatgctctgttcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
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ttttcattttgacagagtcttttttttaatatatactgagcaaaaaaaaacaaatgctaagttgtggcattcttgttgtc-----catgctgtggatgaaaccagGTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG
upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 7
gtgcaattgtgatacctacaaatattgttttgatgctgcctatttaaaatgttaaatg-atggcattctttttttttttcacatgctctgt-tcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
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-tcagattttcattttttgcaatgtt-tttttataccgagtatttttttttccaattctaagttgtgacatttttcttgtctgtgctgtgcataaaaaccagGTAGCGAAGGCTCCTGACGGCAACGGTGGAGTTTATGCTG
upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 8
gtgcaattgtgatacctaca-aatattgttttga--tgctgcctatttaaaatgttaaatgatggcat-tctttttttttttcacatgctctgttcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
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----agctcctatttttttatgaccccattttgaattgtttttaattttatgtatactttggttacatgtccggtggtttaatatttgaaacttttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 7
gtgcaattgtgatacctacaaatattgttttgatgctgcctatttaaaatgttaaatgatggcat-tctttttttttttcacatgctctgttcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
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ctctagctcttattttttatgaccctattttga-attgtgtttttattttattttttggttacatgtctggtggtttaatatttgaaacttttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAGMapped 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|396941374|gb|HO188583.1|HO188583EST: TTCCATGTGTTTCTGCTGATGGCAGATTTATTATGGAGACACCATACAAG GTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
genomic: TTCCATGTGTTTCTGCTGATGGCAGATTTATTATGGAGACACCATACAAGgtaccatctt ... tcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
EST:
gi|428647|gb|D24799.1|D24799EST: TTCCATGTGTTTCTGCTGATGGCAGATTTATTATGGAGACACCATACAAG GTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
genomic: TTCCATGTGTTTCTGCTGATGGCAGATTTATTATGGAGACACCATACAAGgtaccatctt ... tcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatgttaaatgatggcattctttttttttttcacatgctctgttcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
ttctttttttttttca CT-rich tract
attctttttttttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcaattgtgatacctacaaatattgttttgatgctgcctatttaaaatgttaaatgatggcattctttttttttttcacatgctctgttcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG