Sequence
atgc intronic sequence ATGC exonic sequencegtaaggaatatacacaaccgcacagctgtttcgaagcactggttaagtaccattgttgtatttgtttttaattcaactgcgctcttgaattcagGTTCTTGAGGTTCGACCTGTGATAGACTGGAACAAGGGGAAAGCTGTGGAATTTTTGCTGGAGTCACTTGGACTATGTGGGAAAGAAGATGTTCTTCCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os10g40550.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G12430.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaaggaatatacacaaccgcacagctgtttcgaagcactggttaagtaccattgttgtatttgtttttaattcaactgcgctcttgaattcagGTTCTTGAGGTTCGACCTGTGATAGACTGGAACAAGGGGAAAGCTGTGGAATTTTTGCTGGAGTCACTTGGACTATGTGGGAAAGAAGATGTTCTTCCTA
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-------------gtttgtgattagcttaagagatacttagcttacgtttaatcatcggtcttaatttcttgattatcattttttgtgttaaagGTTTTAGAGGTTCGTCCTGTGATAGACTGGAACAAAGGAAGAGCGGTCGAGTTTCTATTAGAATCTCTCG------------------------------
upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv00s0233g00030.t01 (Vitis vinifera), 3'ss of exon 7
-------gtaaggaatatacacaaccgcacagctgtttcgaagcactgg-----ttaagtacca----ttgtt-gtatttgtttttaa-ttcaactgcgctcttga-attcagGTTCTTGAGGTTCGACCTGTGATAGACTGGAACAAGGGGAAAGCTGTGGAATTTTTGCTGGAGTCACTTGGACTATGTGGGAAAGAAGATGTTCTTCCTA
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gtaatattttctccctgaacacccttgcatatttttcctcaagatatggagattttaggcagtggttcttattagtaaatttcatcaacttcatatgttcttcccatgcttagGTTTTAGAGGTCCGTCCTGTGATTGACTGGAACAAGGGGAAAGCAGTTGAATTTCTTCTCGAATCACTTG------------------------------
upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 7
gtaaggaatatacacaaccgcacagctgtttcgaagcactggttaagtaccattgttgtatttgtttttaattcaactgcgctcttgaattcagGTTCTTGAGGTTCGACCTGTGATAGACTGGAACAAGGGGAAAGCTGTGGAATTTTTGCTGGAGTCACTTGGACTATGTGGGAAAGAAGATGTTCTTCCTA
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gtaatctttgga-atgatgttgtagatttttcaatatattatcttcagcttgtccttttcttt--tctgaaccccact-tattaatga--ttagGTTTTAGAGGTCCGACCTGTGATTGACTGGGATAAGGGAAAAGCTGTTGAGTTTTTACTTGAGTCACTTG------------------------------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|33822165|gb|CF336898.1|CF336898EST: CTGCCGTCCTGAAGAATTACCCTTGTCTAAGGCTTACCCATGGGAGAAAG GTTCTTGAGGTTCGACCTGTGATAGACTGGAACAAGGGGAAAGCTGTGGAA
genomic: CTGCCGTCCTGAAGAATTACCCTTGTCTAAGGCTTACCCATGGGAGAAAGgtaaggaata ... ttgaattcagGTTCTTGAGGTTCGACCTGTGATAGACTGGAACAAGGGGAAAGCTGTGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttaagtaccattgttgtatttgtttttaattcaactgcgctcttgaattcagGTTCTTGAGGTTCGACCTGTGATAGACTGGAACAAGGGGAAAGCTGTGGAATTTTTGCTGGAGTCACTTGGACTATGTGGGAAAGAAGATGTTCTTCCTA
ttttaat putative branch site (score: 3)
cgctctt putative PPT
attgttgtatttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggaatatacacaaccgcacagctgtttcgaagcactggttaagtaccattgttgtatttgtttttaattcaactgcgctcttgaattcagGTTCTTGAGGTTCGACCTGTGATAGACTGGAACAAGGGGAAAGCTGTGGAATTTTTGCTGGAGTCACTTGGACTATGTGGGAAAGAAGATGTTCTTCCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG