Nucleotide sequence and molecular evolution of mouse retrovirus-like IAP elements

Aota Shin-ichi; Gojobori Takashi; Shigesada Katsuya; Ozeki Haruo; Ikemura Toshimichi

doi:10.1016/0378-1119(87)90153-3

Nucleotide sequence and molecular evolution of mouse retrovirus-like IAP elements

Aota Shin-ichi^*, Gojobori Takashi, Shigesada Katsuya, Ozeki Haruo, Ikemura Toshimichi

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

Abstract

We determined the nucleotide (nt) sequences of cDNA and genomic clones for murine intracistemal type A particle (IAP) elements, which are retrovirus-like repetitive sequences in rodent genomes. The nucleotide sequence of the cDNA resembled that of retrovirus RNA genomes in its lack of the U5 sequence within the 3′ long terminal repeat. By sequence comparison of our clones with reported rodent IAP elements, we located the probable gag, pol and env gene regions. The sequences for the pal, env and the 3′ two-thirds of the gag region were conserved among the IAP elements. In the regions, synonymous substitutions occurred more frequently than non-synonymous ones, which suggested that the regions in question were functionally constrained until fairly recently. The rate of nucleotide substitutions in the regions was estimated to be 6-10 × 10^-9 nt per site per year, and significantly higher than that of the cellular genes. These rates may exemplify a characteristic of the nucleotide substitutions for an endogenous retrovirus. The sequence homology between the IAP element and IgE-binding factor gene is discussed.

Original language	English (US)
Pages (from-to)	1-12
Number of pages	12
Journal	GENE
Volume	56
Issue number	1
DOIs	https://doi.org/10.1016/0378-1119(87)90153-3
State	Published - 1987
Externally published	Yes

Keywords

M 13 phage vectors
Repetitive sequence
cDNA cloning
endogenous retrovirus
recombinant DNA
retrotransposon
rodents
synonymous substitution
transposition

ASJC Scopus subject areas

Genetics

Access to Document

10.1016/0378-1119(87)90153-3

Cite this

@article{e5651ff5abfc4fc7b64ad96fb0ce4edb,

title = "Nucleotide sequence and molecular evolution of mouse retrovirus-like IAP elements",

abstract = "We determined the nucleotide (nt) sequences of cDNA and genomic clones for murine intracistemal type A particle (IAP) elements, which are retrovirus-like repetitive sequences in rodent genomes. The nucleotide sequence of the cDNA resembled that of retrovirus RNA genomes in its lack of the U5 sequence within the 3′ long terminal repeat. By sequence comparison of our clones with reported rodent IAP elements, we located the probable gag, pol and env gene regions. The sequences for the pal, env and the 3′ two-thirds of the gag region were conserved among the IAP elements. In the regions, synonymous substitutions occurred more frequently than non-synonymous ones, which suggested that the regions in question were functionally constrained until fairly recently. The rate of nucleotide substitutions in the regions was estimated to be 6-10 × 10-9 nt per site per year, and significantly higher than that of the cellular genes. These rates may exemplify a characteristic of the nucleotide substitutions for an endogenous retrovirus. The sequence homology between the IAP element and IgE-binding factor gene is discussed.",

keywords = "M 13 phage vectors, Repetitive sequence, cDNA cloning, endogenous retrovirus, recombinant DNA, retrotransposon, rodents, synonymous substitution, transposition",

author = "Aota Shin-ichi and Gojobori Takashi and Shigesada Katsuya and Ozeki Haruo and Ikemura Toshimichi",

note = "Funding Information: The authorsa rev eryg ratefutlo oneo f ther eferees for critical readingo f the m~usc~pta nd valuable suggestiontso improvet he manuscriptT. his work was supportedb y a grant-in-aidf or scientificr e-searchf rom the Ministry of Education,S ciencea nd Cultureo f Japan.",

year = "1987",

doi = "10.1016/0378-1119(87)90153-3",

language = "English (US)",

volume = "56",

pages = "1--12",

journal = "GENE",

issn = "0378-1119",

publisher = "Elsevier B.V.",

number = "1",

}

TY - JOUR

T1 - Nucleotide sequence and molecular evolution of mouse retrovirus-like IAP elements

AU - Shin-ichi, Aota

AU - Takashi, Gojobori

AU - Katsuya, Shigesada

AU - Haruo, Ozeki

AU - Toshimichi, Ikemura

N1 - Funding Information: The authorsa rev eryg ratefutlo oneo f ther eferees for critical readingo f the m~usc~pta nd valuable suggestiontso improvet he manuscriptT. his work was supportedb y a grant-in-aidf or scientificr e-searchf rom the Ministry of Education,S ciencea nd Cultureo f Japan.

PY - 1987

Y1 - 1987

N2 - We determined the nucleotide (nt) sequences of cDNA and genomic clones for murine intracistemal type A particle (IAP) elements, which are retrovirus-like repetitive sequences in rodent genomes. The nucleotide sequence of the cDNA resembled that of retrovirus RNA genomes in its lack of the U5 sequence within the 3′ long terminal repeat. By sequence comparison of our clones with reported rodent IAP elements, we located the probable gag, pol and env gene regions. The sequences for the pal, env and the 3′ two-thirds of the gag region were conserved among the IAP elements. In the regions, synonymous substitutions occurred more frequently than non-synonymous ones, which suggested that the regions in question were functionally constrained until fairly recently. The rate of nucleotide substitutions in the regions was estimated to be 6-10 × 10-9 nt per site per year, and significantly higher than that of the cellular genes. These rates may exemplify a characteristic of the nucleotide substitutions for an endogenous retrovirus. The sequence homology between the IAP element and IgE-binding factor gene is discussed.

AB - We determined the nucleotide (nt) sequences of cDNA and genomic clones for murine intracistemal type A particle (IAP) elements, which are retrovirus-like repetitive sequences in rodent genomes. The nucleotide sequence of the cDNA resembled that of retrovirus RNA genomes in its lack of the U5 sequence within the 3′ long terminal repeat. By sequence comparison of our clones with reported rodent IAP elements, we located the probable gag, pol and env gene regions. The sequences for the pal, env and the 3′ two-thirds of the gag region were conserved among the IAP elements. In the regions, synonymous substitutions occurred more frequently than non-synonymous ones, which suggested that the regions in question were functionally constrained until fairly recently. The rate of nucleotide substitutions in the regions was estimated to be 6-10 × 10-9 nt per site per year, and significantly higher than that of the cellular genes. These rates may exemplify a characteristic of the nucleotide substitutions for an endogenous retrovirus. The sequence homology between the IAP element and IgE-binding factor gene is discussed.

KW - M 13 phage vectors

KW - Repetitive sequence

KW - cDNA cloning

KW - endogenous retrovirus

KW - recombinant DNA

KW - retrotransposon

KW - rodents

KW - synonymous substitution

KW - transposition

UR - http://www.scopus.com/inward/record.url?scp=0023480535&partnerID=8YFLogxK

U2 - 10.1016/0378-1119(87)90153-3

DO - 10.1016/0378-1119(87)90153-3

M3 - Article

C2 - 3119427

AN - SCOPUS:0023480535

SN - 0378-1119

VL - 56

SP - 1

EP - 12

JO - GENE

JF - GENE

IS - 1

ER -

Nucleotide sequence and molecular evolution of mouse retrovirus-like IAP elements

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this