Sequence
atgc intronic sequence ATGC exonic sequenceGACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTGgtacttttcatattattagaatgaatcattcctttatcttccacctttatttgttatggattgttggctattgatcacttccttagatgatttataccag...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g18310.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 6
GACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTGgtacttttcatattattagaatgaatcattcctttatcttccacctttatttgttatggattgttggctatt-gatcacttccttagatgatttataccag---
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GGTATGCCAGCAGCAGAAGGGGCTGTTGCAGCAGCTGCTGTAGCTGATCAGATGTATGGACCAAAAGAGGACCGCAAGTTGGCCATCGTATTGgtaaaccttgtccacttagaatgc-tcatt---ttaccttttgtagctatgacacagttattgtagattatttaaacttaaagctagataagtgtcttcatttc
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 6
---GACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTGgtacttttcatattattagaatgaatcattccttt-----atcttccacctt-tatttgtta--tggattgttggctattgatcacttccttagatgatt--tataccag------------------------------------------------------------------------------
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AATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTGgtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattag
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 6
---GACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTGgtacttttcatattattagaatgaatcattcctttatcttccacctttatttgttatggattgttggctattgatcacttccttagatgatttataccag------
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AATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTGgtattttc--tgtcattac--tgattgattttgactattcataattttaatgatgctactctattgacaattca--atgtgattggaattcaaacattaaaatcctMapped 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|58689570|gb|CK078257.1|CK078257EST: CTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG GTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGG
genomic: CTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTGgtacttttca ... gccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTGgtacttttcatattattagaatgaatcattcctttatcttccacctttatttgttatggattgttggctattgatcacttccttagatgatttataccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT