Sequence
atgc intronic sequence ATGC exonic sequencegtgcggatcggattcccagtttccccccacatttcgtcgcaatattcaccatagttgaattgaattgccgaatcgtactgaatttttttgaaaaatctgcagGGGAGGTGATCAAGGGGTGGGATGAGGGTATCAAGACGATGAAGAAGGGGGAGCAGGCGGTGTTCACCGTTCCGCCGGAGCTCGCCTACGGCGAGGCCGG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g28420.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g28420.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G11240.1 (Glycine max), 3'ss of exon 1
gtgcggatcggattcccagtttccccccacatttcgtcgcaat--attcaccatagttgaattgaattgccgaatcgtactgaatttttttgaaaaatc--tgcagGGGAGGTGATCAAGGGGTGGGATGAGGGTATCAAGACGATGAAGAAGGGGGAGCAGGCGGTGTTCACCGTTCCGCCGGAGCTCGCCTACGGCGAGGCCGG
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-----aatttattgttatactggacatgaaaattaaacttaagtgattaatgatgaatggat-gaataactatagtattcaatgttttgtgacttgactaatgcagGGCAAGTGATCAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCAGAATTGGCTTATGGAGAGTCAGG
upper sequence: LOC_Os04g28420.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ06798 (Selaginella moellendorffii), 3'ss of exon 2
gtgcggatcggattcccagtttccccccacatttcgtcgcaatattcaccatagttgaatt--gaattgccgaatcgtactgaatttttttg----aaaaatctgcagGGGAGGTGATCAAGGGGTGGGATGAGGGTATCAAGACGATGAAGAAGGGGGAGCAGGCGGTGTTCACCGTTCCGCCGGAGCTCGCCTACGGCGAGGCCGG
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--------------------------------------------------gtgagcgagttatggatttctatctggtgttgatttttctttcttcgtgcttgtgtagGCCAAGTTATCAAGGGATGGGACGAAGGCATTAAGACAATGAAGAAGGGTGAGAACGCGGTGTTCACCATTCCCCCGGCCTTGGCTTATGGAGAAGCTGG
upper sequence: LOC_Os04g28420.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ21868 (Selaginella moellendorffii), 3'ss of exon 2
gtgcggatcggattcccagtttccccccacatttcgtcgcaatattcaccatagttgaattgaattgccgaatcgtactgaatttttttgaaaaatctgcagGGGAGGTGATCAAGGGGTGGGATGAGGGTATCAAGACGATGAAGAAGGGGGAGCAGGCGGTGTTCACCGTTCCGCCGGAGCTCGCCTACGGCGAGGCCGG
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-------------------------------------------gtgagcgagttatggatttctttctggtgttg-atttttctttcttcgtgcttgtgtagGCCAAGTTATCAAGGGATGGGACGAAGGCATTAAGACAATGAAGAAGGGGGAGAACGCGGTGTTCACCATTCCCCCGGCCTTGGCTTATGGAGAAGCTGGMapped 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|2309636|gb|C25791.1|C25791EST: CGATTCCAGCCGCGATCGTGGAACCCCCTTCAAATTCAGCCTCGGCCAAG GGGAGGTGATCAAGGGGT
genomic: CGATTCCAGCCGCGATCGTGGAACCCCCTTCAAATTCAGCCTCGGCCAAGgtgcggatcg ... aaatctgcagGGGAGGTGATCAAGGGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accatagttgaattgaattgccgaatcgtactgaatttttttgaaaaatctgcagGGGAGGTGATCAAGGGGTGGGATGAGGGTATCAAGACGATGAAGAAGGGGGAGCAGGCGGTGTTCACCGTTCCGCCGGAGCTCGCCTACGGCGAGGCCGG
tactgaatttttttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcggatcggattcccagtttccccccacatttcgtcgcaatattcaccatagttgaattgaattgccgaatcgtactgaatttttttgaaaaatctgcagGGGAGGTGATCAAGGGGTGGGATGAGGGTATCAAGACGATGAAGAAGGGGGAGCAGGCGGTGTTCACCGTTCCGCCGGAGCTCGCCTACGGCGAGGCCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT