Sequence
atgc intronic sequence ATGC exonic sequenceATGTCATTTTAAAGGATTGTTTTGTTGGATATTGATTTTGGAATGGCATTGTATTTTCCTCTGCAGGTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacattgctatcctcatgcagtgatgttatctgttaatggaaaagaactgatggagttctgttcaataatag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g38960.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g38960.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G086904_T01 (Zea mays), 5'ss of exon 2
ATGTCATTTTAAAGGATTGTTTTGTTGGATATTGATTTTGGAATGGCATTGTATTTTCCTCTGCAGGTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtaca--cacattgctatcctcatgcagtgatgtta----tctgttaatggaaaagaactgatgga-gttctgttcaataatag----------------
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------------------------------------------------------------------GTATGAGGATGAGCCCCCAGAACCGGAGATTGAGgtgcaggcacattactattgttttatacttttattcaacttctatgctttataggaagatattatatggccaatacaaccaatgtacctctgttgaacag
upper sequence: LOC_Os03g38960.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G013600_T01 (Zea mays), 5'ss of exon 2
ATGTCATTTTAAAGGATTGTTTTGTTGGATATTGATTTTGGAATGGCATTGTATTTTCCTCTGCAGGTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtaca--cacattgctatcctcatgcagtgatgttatctgttaatg------gaaaagaactgatggagttctgttcaataatag----------------
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------------------------------------------------------------------CTATGAGGATGAGCCTCCAGAACCTGAGATTGAGgtgcagacacattactattgttttatacttttattcaacttttatgcttcataggaagagtttatatgac-caatacaatcaatgtacttctgttgaacag
upper sequence: LOC_Os03g38960.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G38350.1 (Glycine max), 5'ss of exon 1
ATGTCATTTTAAAGGATTGTTTTGTTGGAT--ATTGATTTTGGAATGGCATTGTATTTTCCTCTGCAGGTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacattgctatcct-catgcagtgatgttatctgttaatggaaaagaactgatg----gagttctgttcaataatag--------------------------------
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-CGTTGATTCTGTAATCTGTATGTTTTCATTGAATGGTTTCTCA-TGGAATAAAGGGTGGTGGTGCAGGTACGAGGATGAGCCACCAGAGCCCGAGATTGAGgtacagaactctttgtcttgtgtcctttctttttatctgcacaaatacatgttatggtactcagcattgaatgaattaattgaattattggttggtggattgattgatgaacag
upper sequence: LOC_Os03g38960.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G38350.2 (Glycine max), 5'ss of exon 2
ATGTCATTTTAAAGGATTGTTTTGTTGGATATTGATTTTGGAATGGCATTGTATTTTCCTCTGCAGGTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacaca-cattgctatcctcatgcagtgatgttatctgttaatggaaaagaactgatggagttctgttcaataatag
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--------GTACGAGGATGAGCCACCAGAGCCCGAGATTGAGgta-cagaactctttgtcttgtgtcctttctttttatctgc-acaaatacatgttatggtactcagcattgaa----tgaattaattgaattattggttggtggattg--attgatgaacag--------------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|38481397|gb|CF965486.1|CF965486EST: GGTATGAGGATGAGCCACCAGAACCTGAGATTGAG GAAGGGGCTGAAGAGGAAGCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GGTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGTCATTTTAAAGGATTGTTTTGTTGGATATTGATTTTGGAATGGCATTGTATTTTCCTCTGCAGGTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacattgctatcctcatgcagtgatgttatctgttaatggaaaagaactgatggagttctgttcaataatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG