Sequence
atgc intronic sequence ATGC exonic sequence...actgttcgggcacttcactggatgaattataatatctttgtcccaagaacgaataactggattttggcacgactatcttacctagaaatttgctttccagAACGCGCTGGAGCTGACGTTGTTGAGTGCGCGTGTCTCATTGGGCTCCCAAAATTTAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40010.4 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40010.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G071846_T01 (Zea mays), 3'ss of exon 4
--actgttcgggcacttcactggatgaattataatatctttgtcccaagaacgaataactggattttggcacgactatcttacctagaaatttgctttccagAACGCGCTGGAGCTGACGTTGTTGAGTGCGCGTGTCTCATTGGGCTCCCAAAATTTAAG
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gtactgattgtgc-tggaactgtgcca-ccacagtgctgttagcagcatattctctcatcagttcaaactcctcataagtaagctatcaatttgctttccagAACGTGCTGAAGCTGATGTGGTCGAGTGCGCATGCCTCATTGGCCTCCCAAAATTCAAG
upper sequence: LOC_Os02g40010.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G179810_T03 (Zea mays), 3'ss of exon 4
actgttcgggcacttcactggatgaattataatatctttgtcccaagaacgaataactggattttggcacgactatcttaccta-----gaaatttgctttccagAACGCGCTGGAGCTGACGTTGTTGAGTGCGCGTGTCTCATTGGGCTCCCAAAATTTAAG
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-ttggcctgagaaatg--tggac-aatgatacta-ctgtaaagtaatagtgagtattagcccttttttatgtttgagctaattactactacaaattgctttccagAACGTGCTGGAGCCGATGTGGTCGAGTGCGCGTGTGTCATTGGGCTCCCGAAATTCAAG
upper sequence: LOC_Os02g40010.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G179810_T05 (Zea mays), 3'ss of exon 3
actgttcgggcacttcactggatgaattataatatctttgtcccaagaacgaataactggattttggcacgactatcttaccta-----gaaatttgctttccagAACGCGCTGGAGCTGACGTTGTTGAGTGCGCGTGTCTCATTGGGCTCCCAAAATTTAAG-----------------------------------------
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-ttggcctgagaaatg--tggac-aatgatacta-ctgtaaagtaatagtgagtattagcccttttttatgtttgagctaattactactacaaattgctttccagAACGTGCTGGAGCCGATGTGGTCGAGTGCGCGTGTGTCATTGGGCTCCCGAAATTCAAGGTACCGCGTTGCTGGATTCACAACTAATCTGAACTACTGATMapped 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|88211248|gb|CI210888.1|CI210888EST: TGATCTGGTTGCAACTGGTGGGACACTTTGTGCTGCTATAAGGCTTCTTG AACGCGCTGGAGCTGACGTTGTTGAGTGCGCGTGTCTCATTGGGCTCCCAA
genomic: TGATCTGGTTGCAACTGGTGGGACACTTTGTGCTGCTATAAGGCTTCTTGgtacgcacta ... tgctttccagAACGCGCTGGAGCTGACGTTGTTGAGTGCGCGTGTCTCATTGGGCTCCCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaacgaataactggattttggcacgactatcttacctagaaatttgctttccagAACGCGCTGGAGCTGACGTTGTTGAGTGCGCGTGTCTCATTGGGCTCCCAAAATTTAAG
tttgctttcc CT-rich tract
tagaaattt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgttcgggcacttcactggatgaattataatatctttgtcccaagaacgaataactggattttggcacgactatcttacctagaaatttgctttccagAACGCGCTGGAGCTGACGTTGTTGAGTGCGCGTGTCTCATTGGGCTCCCAAAATTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - -gcacttc
- - - - - - - - -ctggatg
- - - - - - - - - - - - - - - - - - - - - - - gaacgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcacgac