Sequence
atgc intronic sequence ATGC exonic sequenceAGAATTCTATGAGGGTTTGAACATGAAAGTGGAACAACAAATTCCCTTGCTGTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAGGCCGAGAAAACTgtaagtgaaatgatcattttataatattctaacagtaatgtacattatttaacttattgttcctttgacctccttaatag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g42820.4 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g42820.4 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G869767_T01 (Zea mays), 5'ss of exon 1
AGAATTCTATGAGGGTTTGAACATGAAAGTGGAACAACAAATTCCCTTGCTGTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAGGCCGAGAAAACTgtaagtgaaatgatcattttataatattctaacagtaatgtacattatttaacttattgttcctttgacctccttaatag-
|||||| ||||||||| ||||||||||||| || |||||| ||||||||| ||||||||||||||||||||||||||||||||||| || |||||| |||||||||| | | || |||| | | || ||| ||| |||| ||| | | ||| | ||
AGAATTTTATGAGGGTATGAACATGAAAGTAGAGCAACAAGCTCCCTTGCTTTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAAGCAGAGAAATCTgtaagtgacaccctttcctt----tattgtgtgaata-tgtggtatatataacatatatccaatgtactctcgtcgattag
upper sequence: LOC_Os03g42820.4 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G342105_T02 (Zea mays), 5'ss of exon 5
AGAATTCTATGAGGGTTTGAACATGAAAGTGGAACAACAAATTCCCTTGCTGTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAGGCCGAGAAAACTgtaagtgaaatgatcat-tttataatattctaacagtaatgtacattatttaacttattgttcctttgacctccttaatag
|||||| ||||||||| ||||||||||||| || |||||| |||||||||| ||||||||||||||||||||||||||||||||||| || |||||| |||||||||| | | ||||| || | || ||| || || | | | || || |
AGAATTTTATGAGGGTATGAACATGAAAGTAGAGCAACAAGTTCCCTTGCTTTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAAGCAGAGAAATCTgtaagtgacaccctttcctttattatgtggtatatataacatatatctaatgtactctcgtcgattag-------------
upper sequence: LOC_Os03g42820.4 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA11G06650.2 (Glycine max), 5'ss of exon 4
AGAATTCTATGAGGGTTTGAACATGAAAGTGGAACAACAAATTCCCTTGCTGTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAGGCCGAGAAAACTgtaagtga-aatg-----atcattttataatattctaacagtaatgtacatt--atttaacttattgttcctttgacctccttaatag--------------------
|||||| ||||| ||||| || |||||| |||| ||||||||||| |||| ||||||||| ||||||| | ||||| || ||||||| || || | |||||||| |||| | | | || |||| | | ||| || ||| || ||| | | || | | |
AGAATTTTATGAAGGTTTAAATATGAAATTGGAGCAACAAATTCCTATGCTCTTGGTTGAGAGACAAGCGCTGAATGAGGCTATGGAGGGAGAAAAGAATgtaagtgttaatgtgtttaacttcccatttcattcatggaatgctgttatttctattctttctagtgtcctgtcgaaatgttcttttatttctcactattgaatgtag
upper sequence: LOC_Os03g42820.4 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 5'ss of exon 9
AGAATTCTATGAGGGTTTGAACATGAAAGTGGAACAACAAATTCCCTTGCTGTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAGGCCGAGAAAACTgtaag---tgaaatgatcattttataatattctaacagtaatgtacattatttaacttattgttcctttgacctccttaatag----------------------------
|||||| |||||||||||||| ||||||||||| || ||| | || | || ||||||||| ||||||| ||||||| |||||||||| || || | |||||| | | | | | || || || | | || || | | | | | || || || | ||| | |
AGAATTTTATGAGGGTTTGAATATGAAAGTGGAGCAGCAAGTCCCTCTTCTCTTGGTTGAGAGACAAGCACTAAATGAGGCCATGGAGGGAGAAAAGAATgtaagggctaatgcattgaagtgatcat-ttttcatagcaacaggtactttcttgtcttttatt--ttaagcttccatcaagtttgaatgttctctttattttatgggcag
upper sequence: LOC_Os03g42820.4 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 5'ss of exon 12
AGAATTCTATGAGGGTTTGAACATGAAAGTGGAACAACAAATTCCCTTGCTGTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAGGCCGAGAAAACTgtaag------tgaaatga--tcattttataatattctaacagtaatgtacattattta-acttattgttcctttgacctccttaatag--------------------
|||||| |||||||||||||| ||||||||||| || ||||| || | || ||||||||| ||||||| ||||||| |||||||||| || || | |||||| || | ||| | || ||| || | ||||| ||| | | || | || ||| | ||| | | |||
AGAATTTTATGAGGGTTTGAATATGAAAGTGGAGCAGCAAATCCCTCTTCTCTTGGTTGAGAGACAAGCACTAAATGAGGCCATGGAGGGAGAAAAGAGTgtaaggactaatgcattgaagtgatcatatttcataccaacaggaattttctcgtcttgtattttaagtttccatgaagtt-tgaatgttctctttattgtatgggcagMapped 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|2311882|gb|C28037.1|C28037EST: TGTTGGTTGAGCGACAAG-TTTAAATGAAGCCATGGAGGCCGAGAAAACT GGACATCACCTTNCTTGAAACCAGAGG
genomic: TGTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAGGCCGAGAAAACTgtaagtgaaa ... tccttaatagGGACATCACCTTGCT-GAAACCAGAGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGAATTCTATGAGGGTTTGAACATGAAAGTGGAACAACAAATTCCCTTGCTGTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAGGCCGAGAAAACTgtaagtgaaatgatcattttataatattctaacagtaatgtacattatttaacttattgttcctttgacctccttaatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG