Sequence
atgc intronic sequence ATGC exonic sequence...attttttccccctttatgctatactggaattatttgagcaactgtaaccaagctctgtatgctgatatgctctaaaccaccactgcattggtccttgcagATTTGTTGTAATAGATCTGTCAGCAGGCCCTTGTACGTATGGAAAAATAGAAACTGAAGAGGGCAGTGTGAGTTATAGGTCATTGCCACGGCTATTAAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g19690.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G135968_T01 (Zea mays), 3'ss of exon 5
------------attttttccccctttatgctatactggaattatttgagcaactgtaaccaagctctgtatgctgatatgctctaaaccaccactgcattggtccttgcagATTTGTTGTAATAGATCTGTCAGCAGGCCCTTGTACGTATGGAAAAATAGAAACTGAAGAGGGCAGTGTGAGTTATAGGTCATTGCCACGGCTATTAAAT
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tttgcactttggagttgttttcttttaatgatgcacttcaattgttcaagcagctttaaattattt------------gtgctctaaactcccacttgattggcctctgcagATTTGTTGTAATAGATCTTTCAGCGGGCCCTTGTACATATGGGAAAATAGAAACTGAAGAAGGCAGTGTCAGCTATAGGTCAATGCCACGGCTGTCACAA
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G16180.2 (Arabidopsis thaliana), 3'ss of exon 5
attttttccccctttatgctatactggaattatttga-gcaactgtaacc--aagctct--gtatgctgatatgctctaaaccaccactgcattggtccttgcagATTTGTTGTAATAGATCTGTCAGCAGGCCCTTGTACGTATGGAAAAATAGAAACTGAAGAGGGCAGTGTGAGTTATAGGTCATTGCCACGGCTATTAAAT
| | || || | ||| |||| || |||| | | ||||||| ||| | ||| ||| | | | | | | | | |||| |||||| |||||| |||| || || |||||||| ||||| || || |||||||||||||||||||| ||| || || ||||| || || |||
agatattgttggcgtaactatttctgttcttatctggtataacttttcctctaagctctcaacatgattgtat-ttctgatttatctcccctt----cttgatagATATGTTGTCATAGATTTGTCTGCGGGGCCTTGTACATATGGGAAGATTGAAACTGAAGAGGGCAGTGTTAGTCCCAGAACAGTGCCAAGGATACGAAAC
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0077g00820.t01 (Vitis vinifera), 3'ss of exon 5
attttttccccctttatgctatactggaattatttgagcaactgtaaccaagctctgtatgctgatatg---ctctaaacc--accactgcattggtccttgcagATTTGTTGTAATAGATCTGTCAGCAGGCCCTTGTACGTATGGAAAAATAGAAACTGAAGAGGGCAGTGTGAGTTATAGGTCATTGCCACGGCTATTAAAT
||| ||| ||| || ||||| | | ||| || || | | | |||| || | | | || | | |||||||||||| || || || |||||||| ||||| || |||||||| || ||||||||||| || ||||| |||| | || | |||||| | |||
---tttagaggttttttgccg--cttgaattttgaggacaatgtacttttagtcctccacatctctctctctctctcaatctaatttcctgcctgtactattcagATTTGTTGTCATCGACCTCTCAGCAGGGCCTTGCACATATGGAAAGATTGAAACTGAAGAAGGAAGTGTCAGTTCAAAAACACTCCCACGGTTGCGGAATMapped 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|25800195|gb|CA756156.1|CA756156EST: TACCGTTACAATGGTGGTGGTGCAACTCAAGTATGGCTGAGTTCTGGAAG ATTTGTTGTAATAGATCTGTCAGCAGGCCCTTGTACGTATGGAAAAATAGA
genomic: TACCGTTACAATGGTGGTGGTGCAACTCAAGTATGGCTGAGTTCTGGAAGgtgattgttc ... gtccttgcagATTTGTTGTAATAGATCTGTCAGCAGGCCCTTGTACGTATGGAAAAATAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccaagctctgtatgctgatatgctctaaaccaccactgcattggtccttgcagATTTGTTGTAATAGATCTGTCAGCAGGCCCTTGTACGTATGGAAAAATAGAAACTGAAGAGGGCAGTGTGAGTTATAGGTCATTGCCACGGCTATTAAAT
ctctaaa putative branch site (score: 3)
tccttgc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttttccccctttatgctatactggaattatttgagcaactgtaaccaagctctgtatgctgatatgctctaaaccaccactgcattggtccttgcagATTTGTTGTAATAGATCTGTCAGCAGGCCCTTGTACGTATGGAAAAATAGAAACTGAAGAGGGCAGTGTGAGTTATAGGTCATTGCCACGGCTATTAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG