Sequence
atgc intronic sequence ATGC exonic sequence...atattgtacattttttagcatcgtcatagatgagtctattcttccttcgattttctgttctatgtttgatctttatgctatctttttttctgaactgtagGAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTACCTCAGTGTCCCTTTTTTGTCGAGGTTCCTGCTCTGTGAACTGCTGATAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g46040.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
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|16754364|gb|BM038743.1|BM038743EST: TGGTC-CGGAGCAC-GGGCCGCCCTCGCCGGCGTGGTTAAGGTGAAGCAG GAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTAC
genomic: TGGTCGCGGAGCACGGGGCCGCCCTCGCCGGCGTGGTTAAGGTGAAGCAGgtaacatctg ... tgaactgtagGAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTAC
EST:
gi|88243873|gb|CI242995.1|CI242995EST: TGGCCGCGGAGCACGGGGCCGCCCTCGCCGGCGTGGTTAAGGTGAAGCAG GAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTAC
genomic: TGGTCGCGGAGCACGGGGCCGCCCTCGCCGGCGTGGTTAAGGTGAAGCAGgtaacatctg ... tgaactgtagGAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgattttctgttctatgtttgatctttatgctatctttttttctgaactgtagGAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTACCTCAGTGTCCCTTTTTTGTCGAGGTTCCTGCTCTGTGAACTGCTGATAT
gtttgat putative branch site (score: 5)
tctttatgctatcttt CT-rich tract
tatcttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattgtacattttttagcatcgtcatagatgagtctattcttccttcgattttctgttctatgtttgatctttatgctatctttttttctgaactgtagGAGCCATGAGTGGTGGATAATCAAATTTCAGAAGGTCCTGCAAGATTCTACCTCAGTGTCCCTTTTTTGTCGAGGTTCCTGCTCTGTGAACTGCTGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgct