Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaggataagatttgtttaagatctgttttatcaattgtaggcttttaagaatcttacattgagtttgtaacagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g46020.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g46020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G029038_T01 (Zea mays), 3'ss of exon 2
gtaaaaggataagatttgtttaag--atctgttt---tatcaattgtaggcttttaagaatcttacattg------agtttgtaacagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
||||||| | | || | || | | |||||| ||| || | | | | || | |||| | || || | | |||||||||||||||||||||||||| |||||||||||||||||||| |||| |||| ||||| |||||||||| ||||||||||||||| ||||| |||||||
gtaaaagtgcatgtttaatgtatgtcacctgtttatttattaaatttcgtatcttca-aatcgtccactggaaaacaaactaaaacagATGATTATGGTAAGAGAAGAAAATGATCCTGCTCCAGAAGGAGTTGAGTACAAGCATGGGCTTACTCCTCTAATGAGGGATGCACGCAGGCGACGTTTCC
upper sequence: LOC_Os01g46020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G454830_T01 (Zea mays), 3'ss of exon 3
gtaaaaggataagatttgtttaag--atctgttt---tatcaattgtaggcttttaagaatcttacattgagt------ttgtaacagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
||||||| | | || | || | | || ||| ||| || | | | | || | |||| | || ||| | |||||||||||||||||||||||||| |||||||||||||||||||| |||| |||| ||||| |||||||||||||||||||||||||| ||||| |||||||
gtaaaagtgcatgtttaatgtatgtcacctatttatttattaaatttcgtatcttca-aatcgtccactgaaaaacaaactaaaacagATGATTATGGTAAGAGAAGAAAATGATCCTGCTCCAGAAGGAGTTGAGTACAAGCATGGGCTTACTCCTCCAATGAGGGATGCACGCAGGCGACGTTTCC
upper sequence: LOC_Os01g46020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G147614_T01 (Zea mays), 3'ss of exon 3
gtaaaaggataagatttgtttaag--atctgttt---tatcaattgtaggcttttaagaatcttacattgagt-----ttgtaacagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
||||||| | | || | || | | |||||| ||| || | | | || | |||| | || ||| || |||||||||||||||||||||||||| |||||||||||||||||||| | || |||| ||||| |||||||||||||||||||||||||| ||||| |||||||
gtaaaagtgcatgtttaatgtatgtcacctgtttatttattaaacttcgtatcttca-aatcgtccactgaaaacaaactgaaacagATGATTATGGTAAGAGAAGAAAATGATCCTGCTCCAGAAGGAGTCGAGTACAAGCATGGGCTTACTCCTCCAATGAGGGATGCACGCAGGCGACGTTTCC
upper sequence: LOC_Os01g46020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G46640.1 (Glycine max), 3'ss of exon 2
gtaaaaggataagatttgtttaagatctgttttatcaattgtaggcttttaagaatcttac-----attgagtttg--taacagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
|| | | || | || ||| | | | | || | | | ||| ||| || | || | ||||||||||||||||| || ||| | |||| |||||||||| | |||||| |||| |||||| || ||||| || ||||| ||||| || | ||| | || |
gtcagattcaaataattctttcattcttaatcatactctttgattcatataacgttctaactggttactgcatccaactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTACAGACATGGCCTCACTCCACCCATGAGAGATGCTCGCAAGCGTAGATTTC
upper sequence: LOC_Os01g46020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G55300.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaaaaggataagatttgtttaagatctgttttat---------------caattgtaggct----tttaagaatcttacattgagtttgta-acagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
|||||| | | ||| || | | | |||| |||| | | || | || | | | |||| || | | ||||||||| ||||| || || | ||||||||| || | | ||||||||| ||||||||| ||||||||||||| |||||| |||| | || | || |
gtaaaatcaagttacttgattcatcttttacttatatgcgttaacttctgtaattttggactaaaactcaatatggatgctttgatttggcacacagATGATCATGGTTAGGGAGCCTGGTGATCCTGCGCCTAATACAGTTGAATACAGACATGGTCTAACTCCTCCAATGAAGGATGCTCGAAAGAGGAGATTTC
upper sequence: LOC_Os01g46020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g00700.t01 (Vitis vinifera), 3'ss of exon 2
gtaaaaggata---agatttgtttaagatctgttttat--caattgtaggcttttaagaatcttacattgagtt--tgtaacagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
||| | | | || ||| | | | |||| | || || | || | | || |||| | ||||||||||||||||| ||||||||| |||| |||||||||| | | || || |||||| || |||||||||||||||||||| |||| ||| | || |
gtagagtgctgtttgacattatttgacttttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTCMapped 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|88355167|gb|CI651870.1|CI651870EST: ACAAGACATACAATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAG ATGATTATGGTAAGAGA
genomic: ACAAGACATACAATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaaaggat ... tttgtaacagATGATTATGGTAAGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatctgttttatcaattgtaggcttttaagaatcttacattgagtttgtaacagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
atcttac putative branch site (score: 3)
ttttatcaattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaggataagatttgtttaagatctgttttatcaattgtaggcttttaagaatcttacattgagtttgtaacagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC