Sequence
atgc intronic sequence ATGC exonic sequencegtaaaataatcgtcaggctctaatgctttcagaatgttttagttgtggttgtggcaacctggtgtttgttgcaacaatgcttagctagactgagtcaaatcagatgatttatctatgtagtatatgcttttttttgttctacttataaaaaacattttcttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g02380.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 4
gtaaaataatcgtcaggctctaatgcttt-cagaatgttttagttgtggttgtg-gcaacctggtgtttgttgcaaca-atgcttagctagactgagtcaaatcagatgatt--tatctatgtagtatatgcttttttttgttctacttataaaaaacattttcttg-----ctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
|| || | | || | || | | || || | || ||| |||| | || | |||||| ||| | | || | | | | | | | ||| || | | || || | | | |||||||| | | || | | | | |||||||||| |||||| | || ||||| || ||||||||||| || |||||||||||| | || |||||||| || || || |||||| ||||| || |
gtgaagcatttttctattattgttgaaataccaaacattgttgt-gtgtctgtgtgtaagc--gtgtttattgtatggtgtactcaaattttccca-ttttttaatatgtttagtgtttaattatttttcttatctttttgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA
upper sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 4
gtaaaataatcgtcaggctctaat--gctttcagaatgttttagttgtggttgtggcaac--ctggtgtttgttgcaacaatgcttagctagactg-agtcaaatcagatgat---ttatctatgtagta-tatgctt--ttttttgttctacttataaaaaacattttcttgctt-tagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
|| || | | || | | | | | || || | || ||| | | | | | || | | || || | | | | | | | || | ||| || | || | ||||| |||||||| | | | || | | || |||||||||| |||||| | || ||||| || |||||||||||||| |||||||||||| | || ||||||||||| || || |||||| ||||| || |
gtgaagcatttttctacttattgttgaaataccaaacattgttgt-gtgtctataagcatgattattacatggggtactaaaaatttcccaatttttaatatattttagtgctccgttactaattcattaatttgcttatctttttgttgagacttgatatgtggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCTGGGAACAATTATGAAGTGGGAAATATGATAGCTGAAGCATTGAGCAGAGTTGGTAGAA
upper sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaaaataatcgtcaggctctaatgctttcagaatgttttagttgtggttgtggcaacctggtgtttgttgcaacaatgcttagctagactgagtcaaatcagatgatttatctatgtagtatatgcttttttttgttct-acttataaaaaacattttcttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
| | | | |||| | | | || | || || || | | || |||||| |||| | || | | ||| | |||||||||||||||| || || |||||||| ||||| ||||| || |||||||| ||| | || |||||||| ||||| || ||| || ||||| | |
------------------------------------------------------------------------------gtattgtt-gacttaattagattct-taatctagctct-tttcatgtgctttagaggattcttgatcatgtagctcttttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA
upper sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaaaataatcgtcaggctctaatgctttcagaatgttttagttgtggttgtggcaacctggtgtttgttgcaacaatgcttagctagactgagtcaaatcagatgatttatctatgtagtatatgcttttttttgttctacttataaaaaacattttcttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
| || | | | | || || | ||| ||||| | | ||||| | || | | | | | | ||||||||||||||||| ||||| |||||||| || || ||||| || ||||| | ||||| || |||||||| || || || |||||||| || |||||||
------------------------------------------------------------------------------gttt---caaatttatagaactctctttcttttaatatgtta---agagtctttttcaaaaggttctgaatgtaagtcatgtcgatgtagGTTGAAGACAGTGAACTTGCAGATGTTGCAGCTGTTAGTGCGGGTAACAACGACGAAATTGGAAATATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA
upper sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
gtaaaataatcgtcaggctctaatgctttcagaatgttttagttgtggttgtggcaacctggtgtttgttgcaacaatgcttagctagactgagtcaaatcagatgatttatctatgtagtatatgcttttttttgttctacttataaaaaacattttcttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
|||| | | ||| ||||| | || | || ||| | | ||| | | | | | | || | ||| || | | || || | | | | | | ||| | |||| | | | | | ||||||||||||||||||| || |||||||| || || ||||| || ||||| ||||| | || |||||||| || || || ||||| || || || | |
-----gtaattgagaaatacta----tttcaaggtctt---gcgttgattgaga----attatgtctctagtc-tagtcttaagttcatttga---aattttaaaagttcatttttac----ttttatctagaatgtctaggatctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA
upper sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaataatcgtcaggctctaatgctttcagaatgttttagttgtggttgtggcaacctggtgtttgttgcaacaatgcttagctagactgagtcaaatcagatgatttatctatgtagtatatgcttttttttgttctacttataaaaaacattttcttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
| | || | | | || |||| || | |||| | || || | | | | ||| ||| | || | | ||| || |||| |||||||||||||||| || || ||||| |||||||| ||||| || ||||| |||||| | || |||||||||| || |||||| | | |||||||| |
-------------------------------------------------------------gaactgattttagc--ttctaagct-gagtattgaaaattttgcgtttgggctttcca-tgtggattttggaatgtattttttgtcataaatataactttgc---agGTTGAAGACAGTGAACTAGCAGATGTGGCTGCAGTTAGTGCAGGAAACAACTATGAAGTAGGATATATGATAGCTGAAGCTATGGGTCAAGTTGGCAGAAMapped 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|58587940|gb|CF986248.1|CF986248EST: AGAAAACTGCGAAAGCACTAGTTGAAGAGCTAAAGAAATTGTCAAAGGAG GTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAAT
genomic: AGAAAACTGCGAAAGCACTAGTTGAAGAGCTAAAGAAATTGTCAAAGGAGgtaaaataat ... cttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAAT
EST:
gi|33797089|gb|CF324410.1|CF324410EST: AGAAAACTGCGAAAGCACTAGTTGAAGAGCTAAAGAAATTGTCAAAGGAG GTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAAT
genomic: AGAAAACTGCGAAAGCACTAGTTGAAGAGCTAAAGAAATTGTCAAAGGAGgtaaaataat ... cttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtagtatatgcttttttttgttctacttataaaaaacattttcttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
cattttcttgcttt CT-rich tract
ttttttttgttctact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaataatcgtcaggctctaatgctttcagaatgttttagttgtggttgtggcaacctggtgtttgttgcaacaatgcttagctagactgagtcaaatcagatgatttatctatgtagtatatgcttttttttgttctacttataaaaaacattttcttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG