Sequence
atgc intronic sequence ATGC exonic sequenceTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGGgtatgtctccagtcctgcaataggagtatgtctgaaaataggtttttactgactagttttcctggaaaattag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g54640.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G004352_T01 (Zea mays), 5'ss of exon 6
TCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGGgtatgt--ctccagtcctgcaataggagtatgtctgaaaataggtttttactgactagttttcctg--gaaaattag-
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TCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCAGGAGAGGATTGCTAGGCATGAAGCTGCTCATTTCCTAGgtatgtgattctcatttcctagcaaaattatatctgcag-tagtaatttactaaatggatgttctgttgaaaatccag
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G14970.1 (Glycine max), 5'ss of exon 6
TCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGGgtat---gtctccagtcctgcaataggagtatgtctgaaa--------ataggtttttactgactagt---tttcctggaaaattag--------------
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GCTTCTCCAAGCTGCTATTGGCAGCTTTTCAACACTTTTTCCTGATTATCAAGAAAGGATTGCCAGGCATGAAGCTGCTCACTTTTTGAgtactgcacttttttttttgctgttttttttcgctcacaatgcatcagatatgttactgtgctctaacccattttctgtttggtcttctgtttcattctag
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G31720.1 (Glycine max), 5'ss of exon 6
TCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGGgtatgtctccagtcctg-------------caataggagtatgtctgaaa-ataggtttttactgactagttttcctggaaaattag-------------
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GCTTCTCCAAGCTGCTATTGGCAGCTTTTCAACACTTTTTCCTGATTATCAAGAAAGGATTGCCAGGCATGAAGCAGCTCACTTTTTGAgtactgcccttttcttttttggctggttttcatgcacaatgcatcagatatgtgactttgctctaacccattttctgtttggtcttgtgtttcattctag
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 5'ss of exon 6
TCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGGgtatgtctccagtcctgcaata----ggagtatgt-ctgaaaataggtttttactgact--agttttcctggaaaattag--------------------
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GCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCAGGAGAGGATTGCTAGACATGAAGCAGCCCATTTTTTAGgtaacctctctgtgctgaaatatccaataccatgcaccaaacatcagctacgcttgattccagcataaaatgaatatgaaatcccgtgcttaatctattaMapped 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|38476935|gb|CF961068.1|CF961068EST: TCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGG TTGCCTATTTGATTGGACTACCAATTCTGGGATATTCCTTGGACATTGGAA
genomic: TCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGGgtatgtctcc ... ggaaaattagTTGCCTATTTGATTGGACTACCAATTCTGGGATATTCCTTGGACATTGGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGGgtatgtctccagtcctgcaataggagtatgtctgaaaataggtttttactgactagttttcctggaaaattag
- - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT