Sequence
atgc intronic sequence ATGC exonic sequencegttcttatttttgctcaatttagcgaatagctctttccctgaaaagatccttaagtatgttgagagtcagcagcaattctagtttcagtcccaatttcgggcactctgtagttcatactgtgtgtcttttgatttttttttgaatgaatttgatatttgatagaatgttaagccactccactttgttcgtgcagGTTTCTTTTGAGGATAAGAAAAAAGAGTTGTTTGAGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g06810.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g06810.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 12
gttcttatttttgctcaatttagcgaatagctctttccctgaaaagatccttaagtatgttgagagtcagcagcaattctagtttcagtcccaatttcgggcactctgtagttcatactgtgtgtcttttgatttttttttgaatgaatttgatatttgatagaatgttaagccactccactttgttcgtgcagGTTTCTTTTGAGGATAAGAAAAAAGAGTTGTTTGAGATG-------------------------------------------------------------
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gttcttgtttctcttcaatttcttggatg--ttttttcttgtat--attttccgcattgttaagaactaaaatctact----tatttgtacccattttgtactcaccccagttcttact----------tgatggccttttgagctaacaagg-attttgtagaatgctaaactgttttttttttgttatgcagGTTTCTTTCGAAGACAAGAAAAAAGAGTTGTTTGAGATGGTATTACTGAAATATGTCATGATTTCTATGTTTTATTAAAAAGTTTGGTACCTACTACTGT
upper sequence: LOC_Os12g06810.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G167999_T01 (Zea mays), 3'ss of exon 12
gttcttatttttgctcaatttagcgaatagctctttccctgaaaagatccttaagtatgttgagagtcagcagcaattctagtttcagtcccaatttcgggcactctgtagttcatactgtgtgtcttttgatttttttttgaatgaatttgatatttgatagaatgttaagccactccactttgttcgtgcagGTTTCTTTTGAGGATAAGAAAAAAGAGTTGTTTGAGATG
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gttcttgtttctcttcaatttcttggatg--ttttttcttgtat--attttccgcattgttaagaactaaaatctact----tatttgtacccattttgtactcaccccagttcttact----------tgatggccttttgagctaacaagg-attttgtagaatgctaaactgttttttttttgttatgcagGTTTCTTTCGAAGACAAGAAAAAAGAGTTGTTTGAGATG
upper sequence: LOC_Os12g06810.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 11
gttcttatttttgctcaatttagcgaatagctctttccctgaaaagatccttaagtatgttgagagtcagcagcaattctagtttcagtcccaatttcgggcactc-tgtagttcatactgtgtgtcttttgatttttttttgaatgaatttgatatttgatagaatgttaagccactccactttgttcgtgcagGTTTCTTTTGAGGATAAGAAAAAAGAGTTGTTTGAGATG
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------------------------------------gtaagaatagattgtactttcatttggttatcggt-gtggcaaca-ttgtagaaaggaatgaacatacttgtattgattataat-tataattttcgaagttctattgagttca--aaatagctcat-----gctttacatgtgaactatgt--atgtagGTTTCATTTGAGGAGAAGAAAGAAGAGTTGTTTGAGATGMapped 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|2311999|gb|C28154.1|C28154EST: TCAAATTGTGGGAGATTACTCGAGGAGCTGTTATTGAAGACTTTGGCAAG GTTTCTTTTGAGGATAAGAAAAAAGAGTTGTTTGAGATG
genomic: TCAAATTGTGGGAGATTACTCGAGGAGCTGTTATTGAAGACTTTGGCAAGgttcttattt ... gttcgtgcagGTTTCTTTTGAGGATAAGAAAAAAGAGTTGTTTGAGATG
EST:
gi|88225951|gb|CI225867.1|CI225867EST: TCAAATTGTGGGAGATTACTCGAGGAGCTGTTATTGAAGACTTTGGCAAG GTTTCTTTTGAGGATAAGAAAAAAGAGTTGTTTGAGATG
genomic: TCAAATTGTGGGAGATTACTCGAGGAGCTGTTATTGAAGACTTTGGCAAGgttcttattt ... gttcgtgcagGTTTCTTTTGAGGATAAGAAAAAAGAGTTGTTTGAGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaatgaatttgatatttgatagaatgttaagccactccactttgttcgtgcagGTTTCTTTTGAGGATAAGAAAAAAGAGTTGTTTGAGATG
atttgat putative branch site (score: 5)
ctttgttc putative PPT
aatttgatatttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttatttttgctcaatttagcgaatagctctttccctgaaaagatccttaagtatgttgagagtcagcagcaattctagtttcagtcccaatttcgggcactctgtagttcatactgtgtgtcttttgatttttttttgaatgaatttgatatttgatagaatgttaagccactccactttgttcgtgcagGTTTCTTTTGAGGATAAGAAAAAAGAGTTGTTTGAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG