Sequence
atgc intronic sequence ATGC exonic sequencegtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatagTTGTTGAGCGAATCTCTGGGAAAGACAACATCCTAAATCATCTAAGCATCCCGGCTGCCTGTTTCACTCATCCGGAGATTAGTATGGTTGGGCTAACAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g23610.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
gtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatagTTGTTGAGCGAATCTCTGGGAAAGACAACATCCTAAATCATCTAAGCATCCCGGCTGCCTGTTTCACTCATCCGGAGATTAGTATGGTTGGGCTAACAGA
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-------gtaaatgttgtgctcacctgtttcttttatc------catgctcgatgct--------gatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 10
gtagatacagaataatttgttcactgttttattgtacttca-gcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatagTTGTTGAGCGAATCTCTGGGAAAGACAACATCCTAAATCATCTAAGCATCCCGGCTGCCTGTTTCACTCATCCGGAGATTAGTATGGTTGGGCTAACAGA
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--------------------------gtaagtggtaactgatgtaacttttccaaaatttagtttatgc-agcaatatcatttgatgaaaaaat---tgtctaa---cagTGGTTGAACAAGTCACTGGAAAAGATCACGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAACTTAGCATGGTTGGATTAACAGA
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 10
gtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatagTTGTTGAGCGAATCTCTGGGAAAGACAACATCCTAAATCATCTAAGCATCCCGGCTGCCTGTTTCACTCATCCGGAGATTAGTATGGTTGGGCTAACAGA
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----------------gtaagtggtaactcatgtaattttcccaaaaattttagtttttgctgcaat--------atcatttgatgaaaaaat---tgtctaa---cagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatagTTGTTGAGCGAATCTCTGGGAAAGACAACATCCTAAATCATCTAAGCATCCCGGCTGCCTGTTTCACTCATCCGGAGATTAGTATGGTTGGGCTAACAGA
aactaat putative branch site (score: 2)
tttcttgtct CT-rich tract
tttgataactaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatagTTGTTGAGCGAATCTCTGGGAAAGACAACATCCTAAATCATCTAAGCATCCCGGCTGCCTGTTTCACTCATCCGGAGATTAGTATGGTTGGGCTAACAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT