Sequence
atgc intronic sequence ATGC exonic sequence...atccttggaaatttttgcttgtaaagtactagctcctctggggataatgttcatatattatacatgttagcatgactattaataattaatatggtgctagGAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTACTTTCAATGAAGAACTTTATACCACAAAGCTAGAGAGAGGTCCTCACATG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g27950.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g27950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G829738_T01 (Zea mays), 3'ss of exon 5
atccttggaaat--ttttg---cttgtaaagtactagctcctctggggataatgttcatatattatacatgttagcatgactattaat--aattaatatggtgctagGAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTACTTTCAATGAAGAACTTTATACCACAAAGCTAGAGAGAGGTCCTCACATG
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-tcaatggaaatagtgttggaacatctgaaacattatttcctttggttgta----caaggcttcatgataattagta--aatattaatccattccatacatttgcagGAGCTGGGACCAGTTTGAAACCAATGCAGCATTATTTGGGGTAAAGAGTACTTTCAATGAAGAAATTTATACCACAAAGCTTGAGAGAGGTCCTCACATG
upper sequence: LOC_Os02g27950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G056773_T01 (Zea mays), 3'ss of exon 5
atccttggaaatttttgcttgtaaag-tact-----agctcctctggggataatgttcatatattatacatgttagcatgactattaataattaatatggtgctagGAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTACTTTCAATGAAGAACTTTATACCACAAAGCTAGAGAGAGGTCCTCACATG
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---cctaagtgcttgcatcgatagaactactgctgaaacatctctgac-attatttgctttggttgtacacggctgcatgat--ataacaatccatagatttgcagGAGCTGGGATCAGTTCGAAACCAATGCAGCCTTGTTTGGGGTAAAGAGTACATTCAATGAAGAAATTTATACCACAAAGCTTGAGAGAGGTCCTCATATG
upper sequence: LOC_Os02g27950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G03190.1 (Glycine max), 3'ss of exon 5
atccttggaaatttttgcttgtaaagtactagctcctctggggataatgttcatatattata--catgttagcatg-actattaataatt-aatatggtgctagGAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTACTTTCAATGAAGAACTTTATACCACAAAGCTAGAGAGAGGTCCTCACATG
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-tttttcagaagtatattttcca---ttttttttttcctaatttcaatttttacacaaaatgtccattttggtttacattgttttttccccggtatttttaaagGGGATGGGATCAGTTTGAAACAAATGAGGCATTGTTTGGTGTAAAAAGCACATTCAATGAGGACCTTTATACAACAAAGCTTGAAAAAGGGCCTCAGACA
upper sequence: LOC_Os02g27950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G42230.1 (Glycine max), 3'ss of exon 5
---atccttggaaatttttgctt-gtaaagtactagctcctctggggataatgttcatatattatacatgttagcatgactattaataattaatatggtgctagGAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTACTTTCAATGAAGAACTTTATACCACAAAGCTAGAGAGAGGTCCTCACATG
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ttttttttcagaagtatatgtttcatctctttctaatttcaatttttacacaaaatgtccatttt---tgtttacatttttttttcttttta-tatttttaaagGGGATGGGATCAGTTTGAAACAAATGAGGCATTGTTTGGTGTGAAAAGCACATTCAATGAGGAACTTTATACAACAAAGCTTGAAAAAGGGCCTCAGACAMapped 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|58695730|gb|CK084417.1|CK084417EST: GGGGATTCAGAGTGCATCGAATTGGAAAAATATGACAGAAAGGGGAACAG GAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTAC
genomic: GGGGATTCAGAGTGCATCGAATTGGAAAAATATGACAGAAAGGGGAACAGgtatggctac ... atggtgctagGAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTAC
EST:
gi|58676503|gb|CK065190.1|CK065190EST: GGGGATTCAGAGTGCATCGAATTGGAAAAATATGACAGAAAGGGGAACAG GAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTAC
genomic: GGGGATTCAGAGTGCATCGAATTGGAAAAATATGACAGAAAGGGGAACAGgtatggctac ... atggtgctagGAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgttcatatattatacatgttagcatgactattaataattaatatggtgctagGAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTACTTTCAATGAAGAACTTTATACCACAAAGCTAGAGAGAGGTCCTCACATG
atgactattaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atccttggaaatttttgcttgtaaagtactagctcctctggggataatgttcatatattatacatgttagcatgactattaataattaatatggtgctagGAGCTGGGACCAGTTTGAAACAAATGCAGCTTTGTTTGGGGTAAAGAGTACTTTCAATGAAGAACTTTATACCACAAAGCTAGAGAGAGGTCCTCACATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG