Sequence
atgc intronic sequence ATGC exonic sequenceCTCCCACGGATCCCACGAGTACCACCAGGAGACGCTCGACAACCTCCGCGCCGCCATGGAGAGCACCGGCATCCTCTGCGCCGTCATGCTCGACACCAAGgtcccattcgtgtctccaatcccctccctgcctccctcctcgatctctcggtttaatttttcctcttcttgatctattgttcttgatccgcaatttaagg...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g16960.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g16960.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G003883_T01 (Zea mays), 5'ss of exon 1
CTCCCACGGATCCCACGAGTACCACCAGGAGACGCTCGACAACCTCCGCGCCGCCATGGAGAGCACCGGCATCCTCTGCGCCGTCATGCTCGACACCAAGgtcccattcgtgtctccaatcccctccctgcctccctcctcgatctctcggtttaatttttcctcttcttgatctattgttc----ttgatccgcaatttaagg
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CTCCCATGGCTCCCACGAGTACCACCAGGAGACGCTCGACAACCTGCACGCCGCCATGGAGCTCACCGGGATCCTCTGCGCCGTTATGCTCGACACCAAGgtccttcccccgccctcg-caatctccttaccttccttctcaatccccgcggtctcgtgctacggttcgcgatctgcgatacggtgttgtttccttacctt---
upper sequence: LOC_Os01g16960.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA20G02980.1 (Glycine max), 5'ss of exon 1
CTCCCACGGATCCCACGAGTACCACCAGGAGACGCTCGACAACCTCCGCGCCGCCATGGAGAGCACCGGCATCCTCTGCGCCGTCATGCTCGACACCAAGgtcccattcgtgtctccaatcc--cctccctgcctccctcctcgatctctcggtttaatttttcctcttcttgatctattgt-tcttgatccgcaatttaagg
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CTCCCATGGGTCCCACGAGTACCACCAGGAAACCCTCGACAACCTCCGCGCCGCCATGGAGAACACCGGTATTCTCTGCGCCGTCATGCTCGACACCAAGgcacgatacgaccaccagattcgattttcatattccatattctcccctttttgttcgatttgtatttattttatttatttatattctcatcgccgatttt---
upper sequence: LOC_Os01g16960.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA07G35110.1 (Glycine max), 5'ss of exon 1
CTCCCACGGATCCCACGAGTACCACCAGGAGACGCTCGACAACCTCCGCGCCGCCATGGAGAGCACCGGCATCCTCTGCGCCGTCATGCTCGACACCAAGgt----cccattcg---tgtctccaatcccctccctgcctccctcctcgatctctcggtttaatttt-tcctcttc-ttgatctattgttcttgatccgcaatttaagg
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CTCCCATGGGTCCCACGAGTACCACCAGGAAACCCTCGACAACCTCCGCGCCGCCATGGAGAACACCGGTATTCTCTGCGCCGTCATGCTCGACACCAAGgcacgccccaccagatctgtttttcatattctctcc-cctttttgtttgatttgtgtttatatttatattctcatcgccgattttgttttctttgtttata--------
upper sequence: LOC_Os01g16960.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT5G56350.1 (Arabidopsis thaliana), 5'ss of exon 1
CTCCCACGGATCCCACGAGTACCACCAGGAGACGCTCGACAACCTCCGCGCCGCCATGGAGAGCACCGGCATCCTCTGCGCCGTCATGCTCGACACCAAGgtcccatt-cgtgtctccaatcccctccctgcctccctcctcgatctctcggtttaatttttcctcttcttgatctattgttcttgatccgcaatttaagg----
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CTCTCATGGATCTCATGAATACCATCAAGAGACTCTCGATAATCTTCATCAAGCTATGCTTAACACTGGGATTCTCTGTGCCGTCATGCTCGACACCAAGgttcgattacatgacttccatt--tttatagtttatgttgttttgtttccaatttcatctcctttgacttagat---tcgactgtgatttggaattctagggtttMapped 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|33797277|gb|CF324501.1|CF324501EST: CGCCGCCATGCTCGACACCAAG GGGCCAGAGATCCGAACTGGATTTCTGAAAGATGGAAAACCCGTACAGTTG
genomic: CGCCGTCATGCTCGACACCAAGgtcccattcg ... taaaatacagGGGCCAGAGATCCGAACTGGATTTCTGAAAGATGGAAAACCCGTACAGTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTCCCACGGATCCCACGAGTACCACCAGGAGACGCTCGACAACCTCCGCGCCGCCATGGAGAGCACCGGCATCCTCTGCGCCGTCATGCTCGACACCAAGgtcccattcgtgtctccaatcccctccctgcctccctcctcgatctctcggtttaatttttcctcttcttgatctattgttcttgatccgcaatttaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcttc