Sequence
atgc intronic sequence ATGC exonic sequenceATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaatattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatgttctcgattagctttttgtttcatattactttg...
Basic information
species | Oryza sativa |
transcript | LOC_Os05g16660.3 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G028834_T03 (Zea mays), 5'ss of exon 6
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaata---ttcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatgttc--tcgattagctttttgtttcatattactttg
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ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaataattttttttatttgactgtggttttttttgtagtcattattgttagttt--cattgtatcaacatttggccacttaacattgt-ctaaaggttatgc--
upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaatattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccg--cacttatgttctcgattagctttttgtttcatattactttg
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ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttttaatctgacagtggttgtctctttcagtcatagttg-gtagtattaacagttgaccaggttattgcccatatatgctgtttttattgtata-
upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA09G36870.2 (Glycine max), 5'ss of exon 4
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaa------tattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatgttctcgattagctttttgtttcatattactttg
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ATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGGTATgttctctgttcttcacctcccttttgttttgcttca-tgacatacttttattcaatgaaaccttccgttcgttggagaaattgacaaccatgc-ttatgtta
upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA09G36870.1 (Glycine max), 5'ss of exon 4
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaa------tattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatgttctcgattagctttttgtttcatattactttg
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ATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatgttctctgttcttcacctcccttttgttttgcttca-tgacatacttttattcaatga--aaccttccgttcgttggagaaattgacaaccatgcttat---
upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA12G00510.1 (Glycine max), 5'ss of exon 4
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgt------aatattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatgttctcgattagctttttgtttcatattactttg
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ATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtgtattcactgttcttcacctcccttttgtgttgcatca-taacatacttttattcaatga--aaacttccgttcgttggagaaattgacaaccatgcttat---
upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 7
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgta------atattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatgttctcgattagctttttgtttcatattactttg
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ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctgtgttcttcaactcccttttatattttatca-tgacatacttttattctttgaaaccttctgt-tgtttgatttgttggagaaattg-acaacc---
upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 5'ss of exon 8
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaatattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatg---ttctcgattagctttttgtttcatattactttg-
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ATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAGgtaa-actaacaaaatttgattttgattg-attgatacaatcctcagttgatgagagtgttttttaggctttgttgctgagtgttttttggaatgtattttcag
upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 5'ss of exon 6
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaatattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatgt-tctcgattagctt------tttgtttcatat-tactttg-
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ATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAGgtaa-attaacaacatttggattttgattgattgacacaatcctcacatgatgaggttttgagtgtgtgttttggctctctcactgagtttgtggaatgtatatttcag
upper sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S28_21V6.2 (Physcomitrella patens), 5'ss of exon 2
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaatattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatgttctcgattagctttttgtttcatattactttg-----
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ATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAGgttcgttttggattttattttctgcgc-atgtgt-tgggataagtagtttttg--gacatatgtataagtttggatagatgttt-cccaatatccctctcttactMapped 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|86495724|gb|CI138357.1|CI138357EST: GGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG AAAGTGTTTTGCTTTGAGCTTCAGTTCTTCATGTATAATACGGTGTTAACA
genomic: GGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaatattct ... tgttgttcagAAAGTGTTTTGCTTTGAGCTTCAGTTCTTCATGTATAATACGGTGTTAACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaatattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatgttctcgattagctttttgtttcatattactttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA