Sequence
atgc intronic sequence ATGC exonic sequenceATACTGACATTTCAGTTATCGCCGCTGGTGGAATTGTAGATGGCCGTGGCTATGCTGCTGCATTGGCACTTGGTGCTCAGGGCGTTTGCTTAGGAACTAGgtattcttgcaatcttttctctgcacgagtttctcgatagtccatctgcaatcttttctttgcttaggaactcatagtctgattttcacattactagttccatgaacattcag
Basic information
species | Oryza sativa |
transcript | LOC_Os08g37874.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g37874.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G048616_T01 (Zea mays), 5'ss of exon 4
ATACTGACATTTCAGTTATCGCCGCTGGTGGAATTGTAGATGGCCGTGGCTATGCTGCTGCATTGGCACTTGGTGCTCAGGGCGTTTGCTTAGGAACTAGgtattcttgcaatcttttctctgcacgagtttctcgatagtccatctgcaatcttttctttgcttaggaactcatagtct---gattttcacattactagttccatgaacattcag
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ACTCGAGCATTCCAGTTATTGCCGCTGGCGGAATTGTAGATGGACGTGGCTATGTTGCCGCATTGGCACTCGGTGCCCAAGGTGTTTGTTTAGGAACTAGgtattatctcggtctcttgatt-cactatgtacagggaggttacataatcatcttaatttcttatatatgcttacattacaacgactttcag------------------------
upper sequence: LOC_Os08g37874.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S226_16V6.1 (Physcomitrella patens), 5'ss of exon 5
ATACTGACATTTCAGTTATCGCCGCTGGTGGAATTGTAGATGGCCGTGGCTATGCTGCTGCATTGGCACTTGGTGCTCAGGGCGTTTGCTTAGGAACTAGgtattcttgcaatcttttctctgcacgagtttctcgatagtccatctgcaatcttttctttgcttaggaactcatagtctgattttcacattactagttccatgaacattcag
|||| | || || || || || || ||||| |||||||||||||||| ||||||| | || ||||| || || ||||||||| | || || |||| | || | | ||||| | | || || ||| | || || | | | || || || | | | || | ||
GCTACAACATACCTGTCATAGCAGCAGGAGGTATTGTGGATGGCCGTGGCTATGTTGCTGCACTTGCTCTTGGAGCCCAAGGCGTTTGCATGGGGACCAGgt-tactaata--ccactctctttcccatttgcttgat--tgcacttgagagtatattttcctttgtatccttaagtggtacctctctggtctgaag----------------
upper sequence: LOC_Os08g37874.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ08115 (Selaginella moellendorffii), 5'ss of exon 4
ATACTGACATTTCAGTTATCGCCGCTGGTGGAATTGTAGATGGCCGTGGCTATGCTGCTGCATTGGCACTTGGTGCTCAGGGCGTTTGCTTAGGAACTAGgtattcttgcaatcttttctctgcacgagtttctcgatagtccatctgc--aatcttttctttgcttaggaactcatagtctgattttcacattactagttccatgaacattcag
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AGTATAAGATTCCCGTGATTGCGGCTGGAGGGATCGTTGATGCTCGTGGCTATGTCGCTGCTTTGGCACTTGGTGCGAAGGGAGTTTGCCTTGGAACTAGgta-------aagtgtttcg----aatagttt-ttgagttttcatccgcgaaagcttacatttttcttggaaag-----------------------------------------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|33675736|gb|CF303975.1|CF303975EST: TATGCTGCTGCATTGGCACTTGGTGCTCAGGGCGTTTGCTTAGGAACTAG GTTCTTGACCACTGAAGAAAGTTTTGCACATCCCTTGTATAAGAAAAGGCT
genomic: TATGCTGCTGCATTGGCACTTGGTGCTCAGGGCGTTTGCTTAGGAACTAGgtattcttgc ... gaacattcagGTTCTTGACCACTGAAGAAAGTTTTGCACATCCCTTGTATAAGAAAAGGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATACTGACATTTCAGTTATCGCCGCTGGTGGAATTGTAGATGGCCGTGGCTATGCTGCTGCATTGGCACTTGGTGCTCAGGGCGTTTGCTTAGGAACTAGgtattcttgcaatcttttctctgcacgagtttctcgatagtccatctgcaatcttttctttgcttaggaactcatagtctgattttcacattactagttccatgaacattcag
- - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC