Sequence
atgc intronic sequence ATGC exonic sequencegtatgacatttttgttaacatatgccatcatttatgtaaagagaagaattttccacctcaattttctgtccatctgttgtagGTTTCCATTCATTGCTTGTGAGATATTTACATGTGAAATTGATGTCATTTTGAGGACCCTAGTCGAGGATGAACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g40340.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G470292_T01 (Zea mays), 3'ss of exon 3
gtatgacatttttgttaacatatgccatcattt-atgtaaagagaagaattttccacctcaattttctgtccatctgttgtagGTTTCCATTCATTGCTTGTGAGATATTTACATGTGAAATTGATGTCATTTTGAGGACCCTAGTCGAGGATGAACAG
||||||| ||| | || || | |||| ||||||| ||| || ||| | ||| | | ||||||||| ||||| ||||||| ||| |||||||| || ||||| ||||||||||||||||||||||| ||||||||| ||
gtatgac--cattgatcactagtgttgttattttatgtaaaactctgaagttcccatcca----ttcaa---acttcttgtagGTTCCCATTTATTGCTTCTGAAATATTTACTTGCGAAATCGATGTCATTTTGAGGACCCTAGTAGAGGATGAAGAG
upper sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G806347_T01 (Zea mays), 3'ss of exon 3
gtatgac------atttttgttaacatatgccatcattt-atgtaaagagaagaattttccacctcaattttctgtccatctgttgtagGTTTCCATTCATTGCTTGTGAGATATTTACATGTGAAATTGATGTCATTTTGAGGACCCTAGTCGAGGATGAACAG
||||||| || ||| |||| || |||||| ||||||| ||| || | | | |||| | | | ||||||||| || || ||||||||||| |||||||| |||||||| |||||||||||||||||| |||| ||||||||| ||
gtatgaccattgaatcattgataactagtgttgtcattttatgtaaaatcctgaagttccta--ttcatttgaacttctcc--ttgtagGTTCCCTTTTATTGCTTGTGAAATATTTACTTGTGAAATCGATGTCATTTTGAGGACCTTAGTAGAGGATGAAGAG
upper sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S188_88V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------gtatgacatttttgttaacatatgccatcatttatgtaaagagaagaattttccacctcaattttctgtccatctgttgtagGTTTCCATTCATTGCTTGTGAGATATTTACATGTGAAATTGATGTCATTTTGAGGACCCTAGTCGAGGATGAACAG
| | ||| || | | | | | ||| || || || | || | | | | || | | | ||||||||||||||||| ||||| || || |||||||| || |||||||| || | ||| |||| |||||||| ||
gacttgaatttgtagcaatttgtagttatttcgtaagtttgtaatggtagtctaataatgataaaaacaagggagctaagtctcattaccgcccat-gcagGTTTCCATTCATTGCATGTGAAATTTTCACATGTGAGATAGATGTCATATTCAAGACTTTAGTTGAGGATGAGGAGMapped 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|88695505|gb|CI737543.1|CI737543EST: GCGCTCTTTCAA GTTTCCATTCATTGCTTGTGAGATATTTACATGTGAAATTGATGTCATTTT
genomic: GCGCTCTTTCAAgtatgacatt ... tctgttgtagGTTTCCATTCATTGCTTGTGAGATATTTACATGTGAAATTGATGTCATTTT
EST:
gi|29669991|gb|CB666266.1|CB666266EST: TATGTTGTGGAAGAAGTACCAGATGATGCTGNNNNNNNGCGCTCTTTCAA GTTTCCATTCATTGCTTGTGAGATATTTACATGTGAAATTGATGTCATTTT
genomic: TATGTTGTGGAAGAAGTACCAGATGATGCTGAAAAAAAGCGCTCTTTCAAgtatgacatt ... tctgttgtagGTTTCCATTCATTGCTTGTGAGATATTTACATGTGAAATTGATGTCATTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttatgtaaagagaagaattttccacctcaattttctgtccatctgttgtagGTTTCCATTCATTGCTTGTGAGATATTTACATGTGAAATTGATGTCATTTTGAGGACCCTAGTCGAGGATGAACAG
ttttctgtccatct CT-rich tract
aagaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgacatttttgttaacatatgccatcatttatgtaaagagaagaattttccacctcaattttctgtccatctgttgtagGTTTCCATTCATTGCTTGTGAGATATTTACATGTGAAATTGATGTCATTTTGAGGACCCTAGTCGAGGATGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG