Sequence
atgc intronic sequence ATGC exonic sequence...gataacaactagtaaagttcggtttccttcgtgttttagttgaaacggtttgaatttgatatatgtctcattgtaattgaaattttggttctgcttgcagTGCCTTGCCTAAGACGTGCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAGGAGCTGAGGTAGTTCTCGGTGATGATGAGGACGGTGAAGGCTGGCTTGC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g10290.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G063355_T01 (Zea mays), 3'ss of exon 3
--gataacaactagtaaagttcggtttccttcgtgttttagttgaaacggtttgaatttgatatatgtctcattgtaattgaaattttggttctgcttgcagTGCCTTGCCTAAGACGTGCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAGGAGCTGAGGTAGTTCTCGGTGATGATGAGGACGGTGAAGGCTGGCTTGC------
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tgcctttggactactgaattt--actattttgctgtttaaagcttgtagttttcgaattatctcaaatcattgaaaatttttgatttttttattactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCG------ATGAGGATGGCGAAGGCTGGCTTGCAACACA
upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G818887_T02 (Zea mays), 3'ss of exon 2
gataacaactagtaaagttcggtttccttcgtgttttagttgaaacggtttgaatttgatatatgtc---tcattgtaattga--aattttggttctgcttgcagTGCCTTGCCTAAGACGTGCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAGGAGCTGAGGTAGTTCTCGGTGATGATGAGGACGGTGAAGGCTGGCTTGC------
|| | | || | | | | || || | | | || || ||| || |||||| |||| ||||| | | || ||||||| || |||||||||| | ||| |||| ||||||||||||||||||||||| ||||| ||||||| ||||||| || ||||||||||||||
-----tgcctttggactactgaatttactattttgctgtttaaagcttgtagttttcgaattatctcaaatcattgaaattttttgatttttttattactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCG------ATGAGGATGGCGAAGGCTGGCTTGCAACACA
upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G155177_T01 (Zea mays), 3'ss of exon 2
gataacaactagtaaagttcggtttccttcgtgttttagttgaaacggtttgaattt-gatatatgtc---tcattgtaa---ttgaaattttggttctgcttgcagTGCCTTGCCTAAGACGTGCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAGGAGCTGAGGTAGTTCTCGGTGATGATGAGGACGGTGAAGGCTGGCTTGC------
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-------gcctttggactactgaatttactattttgctgtttaaagcttgtagttttcgaattatctcaaatcattgaaaatttttgattttttttattactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCG------ATGAGGATGGCGAAGGCTGGCTTGCAACACAMapped 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|29638206|gb|CB643215.1|CB643215EST: GAGGAAGCCGTATCTCCCACCTGACAAGCAATTTCTCGTCACCAGGAACG TGCCTTGCCTAAGACGTGCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCACCTGACAAGCAATTTCTCGTCACCAGGAACGgtatgctgat ... ctgcttgcagTGCCTTGCCTAAGACGTGCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAG
EST:
gi|38477977|gb|CF962110.1|CF962110EST: GAGGAAGCCGTATCTCCCACCTGACAAGCAATTTCTCGTCACCAGGAACG TGCCTTGCCTAAGACGCGCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCACCTGACAAGCAATTTCTCGTCACCAGGAACGgtatgctgat ... ctgcttgcagTGCCTTGCCTAAGACGTGCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggtttgaatttgatatatgtctcattgtaattgaaattttggttctgcttgcagTGCCTTGCCTAAGACGTGCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAGGAGCTGAGGTAGTTCTCGGTGATGATGAGGACGGTGAAGGCTGGCTTGC
atttgat putative branch site (score: 5)
ttctgctt putative PPT
attgtaattgaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gataacaactagtaaagttcggtttccttcgtgttttagttgaaacggtttgaatttgatatatgtctcattgtaattgaaattttggttctgcttgcagTGCCTTGCCTAAGACGTGCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAGGAGCTGAGGTAGTTCTCGGTGATGATGAGGACGGTGAAGGCTGGCTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- -aacaact
- - - - - - - - - - - - - cttcgtg