Sequence
atgc intronic sequence ATGC exonic sequenceGCGGAGGCGGCGAGGCGGCCGCAGCCGCAGCCGCAGCCGCGGGAGTGGCGGTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAGgtgagaacgcgccgacccgcccccttccgctgctcgccgcgtgcgtcgcgtggctcgtgagatctgcctcggtccggggcgggatgtgggagggtttcga...
Basic information
species | Oryza sativa |
transcript | LOC_Os02g13110.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 1
GCGGAGGCGGCGAGGCGGCCGCAGCCGCAGCCGCAGCCGCGGGAGTGGCGGTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAGgtga-gaacgcgccgacccgcccccttccgctgctcgccgc-gtgc-gtcgcgtggctcgtgagatctgcctcggtccggggcgggatgtgggagggtttcga-
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GAGCCCGCTGCGGCGGCGGCGCAGCCGCAGCCGCAGCCGCTGGAGTGGCGGTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATGgtaataaattcaaccggccgctggcctcttcggatcggcccagtaccgtcgt-tccctcgcgagatttgg-tcggtccggtgtgt--tccggagaggtttagcg
upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 1
GCGGAGGCGGCGAGGCGGCCGCAGCCG--CAGCCGCAGCCGCGGGAGTGGCGGTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAGgtgagaac-gcgccgacccgcccccttccgctgctcgccgcgtgcgtcgcgtggctcgtgagatctgcctcggtccggggcgggatgtgggagggtttcga
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--GATGAGGTCGTGGCAGCTCCGGCGGGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgttgttcctacgttgttctgtcggat-ccagttgttgatgtctttggattagggtttggttcctttgtttcgatctgtttcggatcatgttctgt
upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 1
GCGGAGGCGGCGAGGCGGCCGCAGCCG--CAGCCGCAGCCGCGGGAGTGGCGGTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAGgtgagaacgcgccgacccgcccccttccgctgctcgccgcgtgcgtcgcgtggctcgtgagatctgcctcggtccgg--ggcgggatgtgggagggtttcga
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--GATGAGGTCGTGGCAGCTCCGGCGAGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgtttggtactacgttgtttgctgtcggatccagttgttgatgtgttcggattagggtttggttccatgctttcgatctgtttcggatcatgttc--
upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 1
GCGGAGGCGGCGAGGCGGCCGCAGCCGCAGCCGCAGCCGCGGGAGTGGCGGTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAGgtgagaacgcgccgacccgcccccttccgctgctcgccgcgtgcgtcgcgtggctcgtgagatctgcctcggtccggggcgggatgtgggag--ggtttcga-----
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GGGGGTGAAGTCAAGGAAGTGGAGGCACCGGCGGAGCCTCTGGAGTGGAGGTTCTCTCAGGTGTTCGGGGAGCGGACGGCGGGGGAGGAAGTTCAGGAAGgt----atatatcgcctc---tcatttctctgatccgtttgattgaagcggtttttgttggttttgatatggattggtgtggattttgggatttgttgttgatctgtMapped 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|9864945|gb|AU100695.1|AU100695EST: GTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAG TTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCA
genomic: GTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAGgtgagaacgc ... cttgtttcagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCGGAGGCGGCGAGGCGGCCGCAGCCGCAGCCGCAGCCGCGGGAGTGGCGGTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAGgtgagaacgcgccgacccgcccccttccgctgctcgccgcgtgcgtcgcgtggctcgtgagatctgcctcggtccggggcgggatgtgggagggtttcga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcgccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgccgcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggcgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgggag