Sequence
atgc intronic sequence ATGC exonic sequenceCTCGTGATCGCTCTCCAAGGCGCCGCAGTGTTTCACCAGTTCGTGGGCGCAGCTACAGCAGGTCACCACGTGGCCGAGGTGGTTCTCCTTATGCTGATGGgtaaggcatattttgttaattttacaattctcgtcttgtatggctttataaatcatatattctttatcattcttatgcatgcctgcttttcaccttttttccag
Basic information
species | Oryza sativa |
transcript | LOC_Os02g54770.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g54770.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G080930_T02 (Zea mays), 5'ss of exon 5
-----------CTCGTGATCGCTCTCCAAGGCGCCGCAGTGTTTCACCAGTTCGTGGGCGCAGCTACAGCAGGTCACCACGTGGC--------CGAGGTGGTTCTCCTTATGCTGATGGgtaaggcatattttgttaattttacaattctcg--tcttgtatggctttataaatcatatattctttatcattcttatgcatgcctgcttttcaccttttttccag
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GAGCTATAGCCCTCGTTATCGCTCTCCAAGGCGCCGTAGTCCTTCGCCAGCTCGCGCGCGCAGCTATAGCAGGTCACCATAGTACAACTGCAACGAgtatgtatctctattgctaatgggtatgcga---atcagtgaaaatacaattctatgttcctggatagctttatagaatacatatatatcacattgccagtgc-----tgttatgcacag---------
upper sequence: LOC_Os02g54770.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G080930_T01 (Zea mays), 5'ss of exon 5
-----------CTCGTGATCGCTCTCCAAGGCGCCGCAGTGTTTCACCAGTTCGTGGGCGCAGCTACAGCAGGTCACCACGTGGC--------CGAGGTGGTTCTCCTTATGCTGATGGgtaaggcatattttgttaattttacaattctcg--tcttgtatggctttataaatcatatattctttatcattcttatgcatgcctgcttttcaccttttttccag
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GAGCTATAGCCCTCGTTATCGCTCTCCAAGGCGCCGTAGTCCTTCGCCAGCTCGCGCGCGCAGCTATAGCAGGTCACCATAGTACAACTGCAACGAgtatgtatctctattgctaatgggtatgcga---atcagtgaaaatacaattctatgttcctggatagctttatagaatacatatatatca-cattgccag----------------------------Mapped 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|117221467|gb|CT859027.1|CT859027EST: AGCTACAGCAGGTCACCACGTGGCCGAGGTGGTTCTCCTTATGCTGATGG AAGAGATGGTGGCAGGTACCGCCGTAGCAGGAGCTAGACCCTGATGCCTGT
genomic: AGCTACAGCAGGTCACCACGTGGCCGAGGTGGTTCTCCTTATGCTGATGGgtaaggcata ... ttttttccagAAGAGATGGTGGCAGGTACCGCCGTAGCAGGAGCTAGACCCTGATGCCTGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTCGTGATCGCTCTCCAAGGCGCCGCAGTGTTTCACCAGTTCGTGGGCGCAGCTACAGCAGGTCACCACGTGGCCGAGGTGGTTCTCCTTATGCTGATGGgtaaggcatattttgttaattttacaattctcgtcttgtatggctttataaatcatatattctttatcattcttatgcatgcctgcttttcaccttttttccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT