Sequence
atgc intronic sequence ATGC exonic sequencegtaagttggattttcttttccctttgttacagggctacaatgttttttatgctttactgatatgatattattttgttttaaagCAATTGTGAGCTTTGGAAAGGTCAATCCTGAACAAAAGGAAAAGGTTGAACAAAACGGAGTGTCCATCTACTCGTGGGAAGAGTTTTTGCAGTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g48910.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 7
gtaagttggattt-tcttttccctttgttacagggctacaatgttttttat--gctttactgatatgatattattttgttttaaagCAATTGTGAGCTTTGGAAAGGTCAATCCTGAACAAAAGGAAAAGGTTGAACAAAACGGAGTGTCCATCTACTCGTGGGAAGAGTTTTTGCAGTTG
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gtaagttcgagaaattttctggctgtgtggataagctataatgcagttgatttgacttactgatagtcattcattttgttttaa-gCACTTGTAAGCTTCGGTAAGGTTGATCCTGGGCACAAGGAAAAAGTTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTG
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G02620.1 (Glycine max), 3'ss of exon 6
gtaagttggattt-tcttttccctttgttacagggctaca-atgtttttt-----atgct-ttac--tgatatgat-attattttgttttaaagCAATTGTGAGCTTTGGAAAGGTCAATCCTGAACAAAAGGAAAAGGTTGAACAAAACGGAGTGTCCATCTACTCGTGGGAAGAGTTTTTGCAGTTG
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gtatgtttcattgattctctccattcgttcctaaaatattcatgtatttggaaagaagcaattaccttaatttatttattaattaattttgtagCACTTGTGAGCTTTGGAAAGGTTACTCCTGAACAAAAGCAAGAAGTTGAAAAGTTTGGATTAGCAAT----------------------------
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 7
gtaagttggattt-tcttttccctttgttacagggcta-caatgtttttt-------atgctttactgatatgat--attattttgttttaaagCAATTGTGAGCTTTGGAAAGGTCAATCCTGAACAAAAGGAAAAGGTTGAACAAAACGGAGTGTCCATCTACTCGTGGGAAGAGTTTTTGCAGTTG
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gtatgtttcattgattctctccattcattcctaaaatatccatgtatttggaaagaaacaattaccttagtttatttattaattaattttgtagCACTTGTGAGCTTTGGAAAGGTTACTCCTGAACAAAAGCAAGAAGTTGAAGAGTTTGGGTTAGCAATGTATTCATGGGATGAATTTTTGCAAGTGMapped 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|29616395|gb|CB621407.1|CB621407EST: GTGCTCAAGACATTTCCAAATGCAACAAAGTATTTGAAGA CAATTGTGAGCTTTGGAAAGGTCAATCCTGAACAAAAGGAAAAGGTTGAAC
genomic: GTGCTCAAGACATTTCCAAATGCAACAAAGTATTTGAAGAgtaagttgga ... tgttttaaagCAATTGTGAGCTTTGGAAAGGTCAATCCTGAACAAAAGGAAAAGGTTGAAC
EST:
gi|29617787|gb|CB622799.1|CB622799EST: GTGCTCAAGACATTTCCAAATGCAACAAAGTATTTGAAGA CAATTGTGAGCTTTGGAAAGGTCAATCCTGAACAAAAGGAAAAGGTTGAAC
genomic: GTGCTCAAGACATTTCCAAATGCAACAAAGTATTTGAAGAgtaagttgga ... tgttttaaagCAATTGTGAGCTTTGGAAAGGTCAATCCTGAACAAAAGGAAAAGGTTGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagggctacaatgttttttatgctttactgatatgatattattttgttttaaagCAATTGTGAGCTTTGGAAAGGTCAATCCTGAACAAAAGGAAAAGGTTGAACAAAACGGAGTGTCCATCTACTCGTGGGAAGAGTTTTTGCAGTTG
tactgat putative branch site (score: 2)
ttttgtttt putative PPT
tttactgatatgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttggattttcttttccctttgttacagggctacaatgttttttatgctttactgatatgatattattttgttttaaagCAATTGTGAGCTTTGGAAAGGTCAATCCTGAACAAAAGGAAAAGGTTGAACAAAACGGAGTGTCCATCTACTCGTGGGAAGAGTTTTTGCAGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA