Sequence
atgc intronic sequence ATGC exonic sequence...gacaaacttgacatacctctcctgtttgctagtatgacacatgctcaattcttcaattgcaaaaataatttatttgatctgttgttgattgacataacagGTTTTGCAAATGTGAGATGCCATACAATCCTGATAACCTTATGATCCAATGTGAGGATTGCTCTGACTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g58530.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g58530.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G01140.1 (Glycine max), 3'ss of exon 2
gacaaacttgacatacctctcctgtttgctagtatgacacatgctcaattcttcaattgcaaaaataatttatttgatct--gttgtt---gattgacataacagGTTTTGCAAATGTGAGATGCCATACAATCCTGATAACCTTATGATCCAATGTGAGGATTGCTCTGACTG
|| || | || ||| ||| || | | ||| | || | | | || | |||| | |||||| ||| ||| ||||| ||| |||||||||||||| ||||| |||||| |||| ||| |||||||||||| ||| |||||||
----aaaatggtaagtagtagcttttttttagaatcg-agaagctgtgggatcttatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG
upper sequence: LOC_Os03g58530.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
-----gacaaacttgacatacctctcctgtttgctagtatgacacatgctcaattcttcaattgcaaaaataatttatttgatctgttgttgattgacataacagGTTTTGCAAATGTGAGATGCCATACAATCCTGATAACCTTATGATCCAATGTGAGGATTGCTCTGACTG
| | || | |||| | | | || | || || | |||| || | | | | || | || ||| || | | |||| ||||||||||||||||||||||||||| || | | ||| | || || ||| ||| || ||
gtctcgttgtgttcga-acttctctttcctctcttggtctcgt-tgtgatcgaa-cttctctttcttctcttgtgttcttaccaagcgctttatt-acgtga-agGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGMapped 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|9865574|gb|AU101324.1|AU101324EST: TTTGAGTACAAAT-TGCCACAGGCAGCTTTGTGCCTGCCCGTATAGCTGT GTTTTGCAAATGTGAGATGCCATACAATCCTGATAACCTTATGATCCAATG
genomic: TTTGAGTACAAATCTGCCACAGGCAGCTTTGTGCCTGACCGTATAGCTGTgtaagaatcc ... gacataacagGTTTTGCAAATGTGAGATGCCATACAATCCTGATAACCTTATGATCCAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caattcttcaattgcaaaaataatttatttgatctgttgttgattgacataacagGTTTTGCAAATGTGAGATGCCATACAATCCTGATAACCTTATGATCCAATGTGAGGATTGCTCTGACTG
gattgac putative branch site (score: 3)
ttcaattgcaaaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacaaacttgacatacctctcctgtttgctagtatgacacatgctcaattcttcaattgcaaaaataatttatttgatctgttgttgattgacataacagGTTTTGCAAATGTGAGATGCCATACAATCCTGATAACCTTATGATCCAATGTGAGGATTGCTCTGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT