Sequence
atgc intronic sequence ATGC exonic sequenceAAGACCTGAAAAAATTGGAATCTGAAGTTTCAAACTATAAAGATGATCCTCGCCTTCCATGTGACATTGCACTGAAGAAAATGGTTACAATATCAGAAAAgtacgactaaatttactataagtatacagattacatacatttaacagaaatagtggtaaacttaaatgggaatactgatattttcatttgcattcttaattcag
Basic information
species | Oryza sativa |
transcript | LOC_Os08g03560.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g03560.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G019225_T01 (Zea mays), 5'ss of exon 6
AAGACCTGAAAAAATTGGAATCTGAAGTTTCAAACTATAAAGATGATCCTCGCCTTCCATGTGACATTGCACTGAAGAAAATGGTTACAATATCAGAAAAgtacgactaaatttactataagtatacagattacatacatttaacagaaatagtggtaaacttaaa----tgggaatactgatattttcatttgcattcttaattcag
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AGGACCTGAAGAAGCTGGAGTCGGAAGTTTCAAACTACAAAGATGATCCACGCCTGCCCTGTGAAATCGCACTGAAGAAAATGGTTGCATTATCTGAAAAgtgcgactgagtttaccg-aaatataatga--gcatgcatttacctaata-actgttacccataaagttgcaaaagaactgaaaattttattggcattcttaattcag
upper sequence: LOC_Os08g03560.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA14G10800.1 (Glycine max), 5'ss of exon 6
AAGACCTGAAAAAATTGGAATCTGAAGTTTCAAACTATAAAGATGATCCTCGCCTTCCATGTGACATTGCACTGAAGAAAATGGTTACAATATCAGAAAAgtacg--actaaatttactataagtatacagattacatacatttaac--agaaatagtggtaaacttaaatgggaatactgat--attttcatttgca---ttcttaattcag--------------
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AAGATTTGAAAAAATTAGAATCTGAAGTTTCCTCCTACAAGGATGATCCCAGGCTACCTTGTGACATTGTTCTAAAGAAAATGGTTGCATTGTCAGAAAAgtaagctactcaaatatctaaaagagtgttctgtgtcaccactgaatgaagaagaaaaaacaaagtcttttgaggccctaaattaattatgtcttgcaagactcttacgtttgcgtttcattgttagMapped 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|33811209|gb|CF331494.1|CF331494EST: CGCCTTCCATGTGACATTGCACTGAAGAAAATGGTTACAATATCAGAAAA GACTGAGCGGAGTGTCTACAATCTTCTGAGGACAAGGGATGCTACGATGAG
genomic: CGCCTTCCATGTGACATTGCACTGAAGAAAATGGTTACAATATCAGAAAAgtacgactaa ... cttaattcagGACTGAGCGGAGTGTCTACAATCTTCTGAGGACAAGGGATGCTACGATGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGACCTGAAAAAATTGGAATCTGAAGTTTCAAACTATAAAGATGATCCTCGCCTTCCATGTGACATTGCACTGAAGAAAATGGTTACAATATCAGAAAAgtacgactaaatttactataagtatacagattacatacatttaacagaaatagtggtaaacttaaatgggaatactgatattttcatttgcattcttaattcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA