Sequence
atgc intronic sequence ATGC exonic sequencegtaggcattgcaaccatatgcctggtacagcaagttaatggacatcagtgatgagttgtttgcatgatctttttgtctcagGCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g27350.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g27350.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G173682_T01 (Zea mays), 3'ss of exon 1
-gtaggcattgcaaccatatgcctggtacagcaagtta-----atggacatcagtg---atgagtt--gtttgcatgatctttttgtctcagGCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAG
|| || ||||| | || || || || || || ||| | || | || | | ||| ||||| |||| |||||||| || ||| |||||| ||||||||||| |||||||| || ||||| ||||| || || |||||||||||||||
gttaagctttgcaggactgcgcttgtggtgaaaacttgttttcgtgtgcacgggtgcctagaagctaagtattgacatgcttattgtcccagGGTTTGATGCAATACCTGGTTCCAAGCTCACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGTAGTCAGATGCTGGTTGCTCAG
upper sequence: LOC_Os03g27350.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G442425_T01 (Zea mays), 3'ss of exon 1
-gtaggcattgca--accatatgcctggtacag---caagttaatggacatcagtgatgagttgtttgcatgatctttttgtctcagGCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAG
||| | ||||| || || || |||| | || | ||| ||| ||| || | || |||| | ||||| ||||||||||||| || ||||||||||| ||||||||||| |||| ||| || ||||| |||||||| ||||||||||||||||||
gttagtctttgcaggactatgtgtgtggtggaaacataattgcatgtccataggtggctagatattgacatg--ttaattgtcccaggctttgatgcaatatctgattccaagctaactagtgatgtgaactagGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG
upper sequence: LOC_Os03g27350.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G064212_T02 (Zea mays), 3'ss of exon 2
-gtaggcattgca--accatatgcctggtacag---caagttaatggacatcagtgatgagttgtttgcatgatctttttgtctcagGCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAG
||| | ||||| || || || |||| | || | ||| || ||| || | || |||||| || ||| ||||||||||||| || ||||||||||| ||||||||||| |||||||| || ||||| |||||||| ||||||||||||||||||
gttagtctttgcaggactatgtgtgtggtggaaacataattgcatgtccacaggtggctagatattgacatgataatt--gtcccagGCTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG
upper sequence: LOC_Os03g27350.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G410085_T01 (Zea mays), 3'ss of exon 1
-gtaggcattgca--accatatgcctggtacag---caagttaatggacatcagtgatgagttgtttgcatgatctttttgtctcagGCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAG
||| | ||||| || || || |||| | || | ||| || ||| || | || |||| | ||||| ||||||||||||| || ||||||| ||| ||||||||||| |||||||| || ||||| |||||||| ||||||||||||||||||
gttagtctttgcaggactatgtgtgtggtggaaacataattgcatgtccacaggtggctagatattgacatg--ttaattgtcccagGCTTTGATGCAATATCTGATTTCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG
upper sequence: LOC_Os03g27350.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G458441_T01 (Zea mays), 3'ss of exon 2
-gtaggcattgca--accatatgcctggtacag---caagttaatggacatcagtgatgagttgtttgcatgatctttttgtctcagGCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAG
||| | ||||| || || || |||| | || | ||| || ||| || | || |||| | ||||| ||| ||||||||| || ||||||||||| ||||||||||| |||||||| || ||||| ||||||||
gttagtctttgcaggactatgtgtgtggtggaaacataattgcatgtccacagGTGGCTAGATATTGACATG--TTAATTGTCCCAGACTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGT------------------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|58653596|gb|CK042276.1|CK042276EST: CGCATTTTTAGAGGACTTCTCATCAAGGATATGGATCACTTACAGGAAAG GCTTTGATGCCATCTCTGATTCCAAGTATACTAGTGATGTAAACTGGGGCT
genomic: CGCATTTTTAGAGGACTTCTCATCAAGGATATGGATCACTTACAGGAAAGgtaggcattg ... tttgtctcagGCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagcaagttaatggacatcagtgatgagttgtttgcatgatctttttgtctcagGCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAG
agttaat putative branch site (score: 4)
tctttttgtctc putative PPT
aagttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggcattgcaaccatatgcctggtacagcaagttaatggacatcagtgatgagttgtttgcatgatctttttgtctcagGCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG