Sequence
atgc intronic sequence ATGC exonic sequence...gaaactactatatctaatcgtcatcaattatatgtacttacttttgaggccatttaaatgtgcatcgctcttgatgtcactgtaaattgtaattatgcagGTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g43570.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 2
gaaactactatatctaatcgtcatcaattatatgtacttacttttgaggc-catttaaatgtgcatcgctct-tgatgtcactgtaaattgtaattatgcagGTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAG
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--ttctgttgtcttctgttttagttgagtctgatcgtttcctttctttttgtgttttgccattctttttgctatgttacttatgctactcttaactgtgcagGTGCGTCTT-GTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAGCTCAAGAAATCTGAAATGCTTCGTAGGGGCCAG
upper sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 3
gaaactact-atatctaatcgtcatcaattat--atgtacttacttttgaggccatttaaatgtgcatcgc-tcttgatgtcactgtaaattgtaattatgcagGTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAG
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--aagtactgataactagctattattctttttctatgaaccaaagcttctgttag--tgattttacttggtgtattgatttaatattatttcatttctgtccagGTGAGAATTTGTAAAGAAAAATCTACTGGAAGCGTATATGCAATGAAAAAGTTAAAGAAATCCGAGATGCTTCGACGAGGGCAG
upper sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 3
gaaactactatatctaatcgtcatcaattatatgtacttacttttgaggccatttaaatgtgcatcgctcttgatgtcactgtaaat--tgtaattatgcagGTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAG
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--atttgtagttattagtagaaatacaaatggcgtattcaatagctgttaaactcttagttatagggactttaatgtgaatgtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAGMapped 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|25799292|gb|CA755253.1|CA755253EST: TTGAAGATTTTGAACTTTTGACAATTATTGGAAGAGGTGCATTTGGCGAG GTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAG
genomic: TTGAAGATTTTGAACTTTTGACAATTATTGGAAGAGGTGCATTTGGCGAGgtacttctga ... aattatgcagGTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaggccatttaaatgtgcatcgctcttgatgtcactgtaaattgtaattatgcagGTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAG
tcttgat putative branch site (score: 4)
tgtaaattgtaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaactactatatctaatcgtcatcaattatatgtacttacttttgaggccatttaaatgtgcatcgctcttgatgtcactgtaaattgtaattatgcagGTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG