Sequence
atgc intronic sequence ATGC exonic sequence...gtttgcttgcttctcatcttcttttcatgataaccgccttgcgtttatcatagtatttcctaatattcctattatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48300.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 11
gtttgcttgcttctcatcttcttttcatgataaccgcct-tgcgtttatcatagtatttcctaatattcctattatgttctgatatga-cttgtttc---catagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
| || || | || |||| | | || || | | | | || || | || | | |||| | ||| | |||| | |||||||||| |||||||| || || || | ||| | |||||||||||||| || ||||||||||||||||| || || || |||||
-----tctctttagaatatggattaaatgaaatctttctgtgactaaaagaaaataatttgtccgatcctcttcatgtgatactataaatttgtgttgcttgcagGTTTGTGGGTTTGATCTATTGAGAAGTCAGGGACGCTCATATGTTTGTGATGTGAATGGATGGAGCTTTGTTAAAAATTCATACAA
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 8
gtttgcttgcttctcatcttcttttcatgataaccgcct-tgcgtttatcatagtatttcctaatattcctattatgttctgatatga-cttgtttc---catagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
| || || | || |||| | | || || | | | | || || | || | | |||| | ||| | |||| | |||||||||| |||||||| || || || | ||| | |||||||||||||| || ||||||||||||||||| || || || |||||
-----tctctttagaatatggattaaatgaaatctttctgtgactaaaagaaaataatttgtctgatcctcttcatgtgatactataaatttgtgttgcttgcagGTTTGTGGGTTTGATCTATTGAGAAGTCAGGGACGCTCATATGTTTGTGATGTGAATGGATGGAGCTTTGTTAAAAATTCATACAA
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 8
--gtttgcttgcttctcatcttcttttcatgat-aaccgccttgcgtttatcatagtatttcctaatattcctattatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
| || ||| | || || | | || | | | ||| | | | ||||| ||| | | ||| || | |||||||||| ||||||||||| || || || ||| | || |||||||||||||| ||||||||||||||||| || ||||| ||||
gaggatgaagtcttaaaaatggtttgtcttagtgaagaaaagaaaatgtttttaagtctgctcctcttctcctactataggtcattcttg-ttgcttgc--agGTTTGTGGATTTGATCTCTTGAGATGCGAGGGACGCTCCTATGTTTGTGACGTGAATGGATGGAGCTTTGTTAAAAACTCACACAA
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 10
--gtttgcttgcttctcatcttcttttcatgataaccgccttgcgtttatcata-gtatttcctaatattcctattatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
| || || | || || | | | || || || || || | || || ||| | | ||| || | |||||||||| ||||||||||| || || || ||| |||| |||||||||||||| ||||||||||||||||| || || || ||||
gaggatgaggttttaaaaatggtttgtctcagtgaagaaaagaaaataattttaagtcttctcttcttctcttactataggtcattcttg-ttgcttgc--agGTTTGTGGGTTTGATCTCTTGAGATGCGAGGGACGATCCTATGTTTGTGACGTGAATGGATGGAGCTTTGTTAAAAATTCACACAA
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 11
gttt-gcttgcttctcatcttcttttcatgata--accgccttgcgtttatcatagtatttcctaatattcctattatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
|| | | ||| || | || | || ||| | | | |||| ||| | | | || | || | | | || ||||||| |||||||||||| || | | ||| ||||| ||||||||||||||||| ||||||||||| |||||||||||||| || ||
gtgtagtttgtttgaaggaatgattacgaaatgttgttacctggaaaagttgaagatattattgtataatgcattagtggaattattt---tcatgtctgcagGTTTGCGGTTTTGATCTCCTACGATCTGAGGGAAGTTCATATGTTTGTGACGTAAATGGATGGAGTTTTGTGAAGAACTCCTATAA
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
gtttgct-tgcttctcatcttct---tttcatgataacc------gccttg--cgtttatcatagtatttcctaatat--tcctattatgttctgatat----gacttgtttc-cat----agGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
|| || | || || ||| || | |||| || | ||| | | |||| || ||| | || || | | | || | || | || | || | |||| ||| |||| ||||| |||||||| || | | ||| || | |||||||||||||| || ||||||||||| |||||||||||||| |||||
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
--------gtttgcttgcttctca-tcttcttttcatgataaccgccttgcgtttatcatagtatttcctaatattcctattatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
| | || | | | | | || || | | ||| | || ||| || | | | | ||| ||| |||| |||| |||||||||| ||||||||||| | ||||| ||| | |||||||| ||||| || ||||||||||| |||||||||||||| ||||
acgcaaccatacatatatttgtaaattctttctttattgagatgagttgttgttaa--atgttatgtctttgttctatttatattttcc-atattgcttgc------agGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 10
gtttgcttgcttc-tcatcttcttttcatgataaccgccttgcgtttatcatagt--atttcctaatattccta-ttatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
| ||||| | | || || |||| || ||| | | || | || | | | |||||| |||| | | | || |||| || || |||||| | | | | | || | |||||||||||||| |||||||| ||||| || || |||||||| |||||
--caacatgctttgtaagctgctcttca--atgttagccaggtatctagtgttgttaggtgcatgatattctcggttatctaacagttcataattaatctgcagGTGTGCGGGTTTGATTTACTCCGATCACAAGGCCGGTCATATGTTTGTGATGTTAATGGGTGGAGTTTCGTTAAGAACTCTTACAA
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S70_284V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------------------------------------------------gtttgcttgcttct-catcttcttttcatgataaccgccttgcgt--ttatcatagtatttcctaatattcctattatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
| || | || | | | || ||| | || | | | ||| ||| ||| | || | | || | | | | |||||||||| |||||| | | | | | || | |||||||| |||||||||||||| ||||| ||||| |||||||| |||||
gtgagcactattttttaacagacccttttagtatttaaaaagaaagagaaaaagaagagaaagaagttaaattccaaaacctcaaggcttacatgaacgtgcgtaagacttctgacatactaggattacttacctgctccggtacttcgaaatgcttctgacaaaa---gggataattgg--cctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAAMapped 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|29674285|gb|CB670560.1|CB670560EST: CTACAGAGAAACAAATGTCAAGAGACGTGTGCAGTGCTTTTAGGCAGATG GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGAC
genomic: CTACAGAGAAACAAATGTCAAGAGACGTGTGCAGTGCTTTTAGGCAGATGgtaagctagc ... gtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcatagtatttcctaatattcctattatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
cttgtttcc CT-rich tract
taatattcctattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgcttgcttctcatcttcttttcatgataaccgccttgcgtttatcatagtatttcctaatattcctattatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- -tgcttgc
- - - - - - - catcttc
- - - - - - - - - - - tttcatg
- - - - - - - - - - - - - - - - - -gccttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttctg