Sequence
atgc intronic sequence ATGC exonic sequence...catgctgctttatctttcattttcactgtgaggtttgctaatcgaattctttttactgggatattcctggattctgactagattgatcatttcaaaacagGAAATAAGTTTGGTGTAAATTGAAAATCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g53900.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ28367 (Selaginella moellendorffii), 3'ss of exon 1
catgctgctttatctttcattttcactgtgaggtttgctaatcgaattctttttactgggatattcctggattctgactagattgatcatttcaaaacagGAAATAAGTTTGGTGTAAATTGAAAATCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACAT--------------------------
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------------------------------------------------------------------------------gtgagtgattcctctggaattcgtagcggattctg---acatcgtgatgctctttcca-gGTGAAATTCACGGCAGAAGAGCTGCGCCGGATCATGGACAAGAAGCACAACATCCGGAACATGTCTGTGATTGCTCATGTCGATCACGMapped 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|86888335|gb|CI303617.1|CI303617EST: GCTGGCACCCGGTCTACAATCTACATCCATGCCTCCCGAGGCCGCGGGAG GAAATAAGTTTGGTGTAAATTGAAAATCACTCACAATGGTTAAGTTTACGG
genomic: GCTGGCACCCGGTCTACAATCTACATCCATGCCTCCCGAGGCCGCGGGAGgtatacacca ... ttcaaaacagGAAATAAGTTTGGTGTAAATTGAAAATCACTCACAATGGTTAAGTTTACGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctttttactgggatattcctggattctgactagattgatcatttcaaaacagGAAATAAGTTTGGTGTAAATTGAAAATCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACAT
tcatttc CT-rich tract
atttcaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgctgctttatctttcattttcactgtgaggtttgctaatcgaattctttttactgggatattcctggattctgactagattgatcatttcaaaacagGAAATAAGTTTGGTGTAAATTGAAAATCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- tgctgct
- - - - - - - tttcatt
- - - - - - - - - - -ttcactg
- - - - - - - - - - - - - - - - - -tgctaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attctga