Sequence
atgc intronic sequence ATGC exonic sequenceAAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaacttgccctcctctgtttgcatcatacttttcctggttttggttgtaactaatttgaattgttatttaaacgctttgttcgcaagaggtgaagg...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g44900.3 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G340749_T01 (Zea mays), 5'ss of exon 1
AAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaacttgccctcctctgtttgcatcatact--tttcctggttttggttgtaactaatttgaattgtt-atttaaacgctttgttcgcaagaggtgaagg
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AAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGGCCTTCTCAAAAGAAGGGTTAGGTCAGCAACCAAAAACAgtaagcacttggacttttttgtttgtgctaccgtactttcctggcttca--tgtacatgtttcgagttgtttatataacatccctgttctaagaacgaggtc-
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 3
lower sequence: AC197122.3_FGT003 (Zea mays), 5'ss of exon 4
AAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaacttgccctcctctgtttgcatcatact--tttcctggttttggttgtaactaatttgaattgttatttaaacgctttgttcgcaagaggtgaagg
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AAAGCAGATTGAACGAGAGATGGAACGATTTAAAGTATGTGAGAAGGAAACAAAAACTAAGGCCTTCTCAAAAGAAGGGTTAGGTCAGCAACCAAAAACAgtaagcacttggacttctttgtttgtgttatcgtactttcctggcttca--tgtacatgtttcgagttgtttataactttatataacatccttgtcctaaga
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G07830.1 (Glycine max), 5'ss of exon 3
AAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaacttg-ccctcctctgtttgcatcatacttttcctg-gttttggttgtaactaatttga--attgttatttaa--acgctttgttcgcaagaggtgaagg----------------------------
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CAAGATTATTGAGCGTGAAATGGAAAGATTCAAGATCTGTGAGAAGGAGACAAAAACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtctttgactcagggaaatacgttttttttttttcttatattttgggcttttctaggtgtattatgattatgcacttatgcttcctctttaggggctgaagaatctcttattctcaatgttttgtgacag
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA16G04690.1 (Glycine max), 5'ss of exon 3
AAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaacttgccctcctc--tgtttgcatcatacttttcctggttttgg------ttgtaactaatttgaattgttatttaaacgctttgttcgcaa----gaggtgaagg------------------------
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CAAGCTAATTGAGCGGGAAATGGAAAGATTTAAGATATGTGAGAAGGAAACTAAGACCAAAGCATTCTCCAAAGAAGGCTTGGGTCAACAGCCTAAGACTgtgagtctttgaccagggaaatattacctttttgtttgttgtagttttaccactttttggagcttttttttggtgttctttgatcgtgtttatgtcaattttggtctgaggaatttgttatctgactttctaatag
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 5'ss of exon 3
AAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaacttgccctcctctgtttgcatcatacttttcctggttttggttgtaactaatttgaattgttatttaaacgctttgttcgcaagaggtgaagg---
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GAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAGCATTCTCCAAAGAAGGGCTGGGCCAACAACCTAAAACTgtaagttttagacactgtct---tgctttctgcccaatgttgaaccaagcacatgaatttctgatagtaattttttaatcatggtctttaatagttatggttc
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S101_120V6.1 (Physcomitrella patens), 5'ss of exon 4
AAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaacttgccctcctctgtttgcatcatacttttcctggttttggttgtaactaatttgaatt-gttatttaaacgctttgttcgcaagaggtgaagg
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GAAGCAGATAGAGAGAGAAATGGAAAGATTTAAAGTATGTGAGAAGGAAACCAAGACAAAAGCATTTTCCAAAGAAGGCCTGGGTCAACAACCTAAAACGgtttgtctctactttcgcgtacatacattccgattgtatgctttatcgaattgatcagctagaatttgcttgggaattgcttcatattgacttagtggaa-
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ20408 (Selaginella moellendorffii), 5'ss of exon 3
AAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaacttgccctcctctgtttgcatcatacttttcctggttttggttgtaactaatttgaattgttatttaaacgctttgttcgcaagaggtgaagg
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GAAGCTCATTGAGCGAGAGATGGAACGATTCAAAGTTTGCGAGAAAGAAACGAAAACGAAGGCGTTTTCGAAAGAAGGTCTAGGCCAGCTTCCGAAAACTgtaagtgct-gccattttagattt---ctttggtctgacacgcaacgattgt--ctag------------------------------------------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|29630458|gb|CB635467.1|CB635467EST: CTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACT GATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
genomic: CTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaactt ... atttgtgcagGATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAAGCAGATTGAACGCGAGATGGAACGATTTAAGGTTTGTGAGAAGGAAACTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaacttgccctcctctgtttgcatcatacttttcctggttttggttgtaactaatttgaattgttatttaaacgctttgttcgcaagaggtgaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA