Sequence
atgc intronic sequence ATGC exonic sequenceTCATACAAATTTGCGGAGGGTCACTTACCTTGTTTTAGATGAGGCAGACCGGATGCTGGATATGGGCTTTGAACCTCAGATTAAGAAAATTGTTTCTCAGgtatgcctcttcttctgaatctattattccattctcaacaattttctaataattatgcttgctacatgttacatgcttttacttatacactgtcaacaga...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g10050.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G143246_T01 (Zea mays), 5'ss of exon 5
TCATACAAATTTGCGGAGGGTCACTTACCTTGTTTTAGATGAGGCAGACCGGATGCTGGATATGGGCTTTGAACCTCAGATTAAGAAAATTGTTTCTCAGgtatgcctcttcttctgaatctattattccattctcaacaat--tttctaataa--ttatgcttgctacatgttacatgcttttacttatacactgtcaacaga
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TCATACAAACTTGCGAAGGGTCACATATCTTGTTTTAGATGAAGCAGACCGGATGCTAGACATGGGATTTGAACCTCAGATTAAGAAAATTGTTTCTCAGgtacgcttttgctgctacatgaaatgttactgcctctgtcctgattcctgaaaaggttgcaattctagaataatgctgtgttaaagtttgacaaaatttg----
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 5'ss of exon 5
TCATACAAATTTGCGGAGGGTCACTTACCTTGTTTTAGATGAGGCAGACCGGATGCTGGATATGGGCTTTGAACCTCAGATTAAGAAAATTGTTTCTCAGgtatgcctcttcttctgaatctattattccattctcaacaattttctaataattatgcttgctacatgttacatgcttttacttatacactgtcaacaga
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CAACACAAACCTACGAAGGGTTACTTATCTTGTTTTGGATGAGGCTGATCGAATGCTTGATATGGGGTTTGACCCTCAGATCCGGAAAATTGTTTCACATgt-----tcgtttacttactcctgtcttc-gtcatatatatgtgtatgctagttgctttgtctataacctttctttttaaacctgtgcag----------
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 5'ss of exon 5
TCATACAAATTTGCGGAGGGTCACTTACCTTGTTTTAGATGAGGCAGACCGGATGCTGGATATGGGCTTTGAACCTCAGATTAAGAAAATTGTTTCTCAGgtatgcctctt-cttctgaatctattattccattctcaa--caattttctaataattatgcttgctacatgttacatgcttttacttatacactgtcaacaga
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TCACACAAACTTGCGAAGGGTCACTTACCTTGTGCTGGATGAGGCTGATCGGATGTTAGATATGGGTTTTGAACCGCAGATTAGAAAAATTGTTTCTCAGgttggtttttgacgattatatttgctaccatctttttatgctaataattggaaagcattttctgctaccttagctcctctttttagaagagagtattaat---Mapped 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|218490551|gb|FG953048.1|FG953048EST: GGATGCTGGATATGGGCTTTGAACCTCAGATTAAGAAAATTGTTTCTCAG ATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAA
genomic: GGATGCTGGATATGGGCTTTGAACCTCAGATTAAGAAAATTGTTTCTCAGgtatgcctct ... gccttttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCATACAAATTTGCGGAGGGTCACTTACCTTGTTTTAGATGAGGCAGACCGGATGCTGGATATGGGCTTTGAACCTCAGATTAAGAAAATTGTTTCTCAGgtatgcctcttcttctgaatctattattccattctcaacaattttctaataattatgcttgctacatgttacatgcttttacttatacactgtcaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcttc