RetrogeneDB ID: retro_rnor_1163

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:99391918..99392534(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Eif4a2
• Ensembl ID: ENSRNOG00000001815
• Aliases: None
• Description: Eukaryotic initiation factor 4A-II [Source:UniProtKB/Swiss-Prot;Acc:Q5RKI1]

Sequence

>retro_rnor_1163
AAAGCAGAGCTTGACATTCAGGTTGTGTTGACTTCTGCCACAATGTCAAGTGATGTACTAGAAATGACCAAAAAATTCAT
GAGAGATTCGATTCGAATTCTGGTGGAGAAGGAAGAATTGACCCTTGAAGGAATTAAACAATTTTATATTAATGTTGAGC
AAGAGGATGGAAGAAGCTGGACACTCTTTGTGACTTGAGTGAGACTTTGACTATCACATATATGTTTATTTTTCTCAATG
CAAGGTGCAAGGTGGATTGGCTCATGGAGAAAATGTATGCCAGGGATTTAACAAGTTTTGCTCCTCATGGTGATGTGGAC
AAGAAGGAAAGAGATGTCATCATGAGGAAATTCTGACGAAGATCAAGCCGTGGTCGGATCACCACTGATTGGTTGACTCG
TGGGATTGACATGCAACAAGTGTCCTTGCTTTTAAACTGTGATCCACCTACCAATCATGAAAATTATATTCATAGAATTG
GCAGAAGCCATCAATTTAGGAGGAAAGGTGTGGATATAACTTTGTTACTGATGAAGACAAGAGGACTCTTCGTGACATTG
AGACTTTCTACAATACTGTAGTGAAGGAAATGTCCATAAATGTGGCTGACCTAATT

Alignment

ORF - retro_rnor_1163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.04 %
• Parental protein coverage: 50.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREE-WK-LDTLCDLYET
          K....IQVVL.SATM..DVLE.TKKFMRD.IRILV.KEELTLEGIKQFYINVE.E..WK.LDTLCDL.ET
Retrocopy KAELDIQVVLTSATMSSDVLEMTKKFMRDSIRILVEKEELTLEGIKQFYINVEQED<WKKLDTLCDLSET

Parental  LTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQ
          LTIT...IFLN.R.KVDWL.EKM.ARD.T..A.HGD.D.KERDVIMR.F...SSR..ITTD.L.RGID.Q
Retrocopy LTITYMFIFLNARCKVDWLMEKMYARDLTSFAPHGDVDKKERDVIMRKF*RRSSRGRITTDWLTRGIDMQ

Parental  QVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAI-NFVTEEDKRILRDIETFYNTTVEEMPMNVADLI
          QVSL..N.D.PTN.ENYIHRIGR...F.RKGV.I.NFVT.EDKR.LRDIETFYNT.V.EM..NVADLI
Retrocopy QVSLLLNCDPPTNHENYIHRIGRSHQFRRKGVDI<NFVTDEDKRTLRDIETFYNTVVKEMSINVADLI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	364.01 RPM
SRP017611_kidney	0.00 RPM	270.82 RPM
SRP017611_liver	0.00 RPM	89.09 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1163 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1163 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1163 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014724	2 retrocopies	retro_btau_258, retro_btau_522,
Canis familiaris	ENSCAFG00000013659	1 retrocopy	retro_cfam_378,
Cavia porcellus	ENSCPOG00000011183	1 retrocopy	retro_cpor_639,
Dasypus novemcinctus	ENSDNOG00000011502	5 retrocopies	retro_dnov_1264, retro_dnov_2018, retro_dnov_2066, retro_dnov_648, retro_dnov_869,
Echinops telfairi	ENSETEG00000018565	3 retrocopies	retro_etel_1174, retro_etel_2164, retro_etel_451,
Homo sapiens	ENSG00000156976	2 retrocopies	retro_hsap_593, retro_hsap_878,
Gorilla gorilla	ENSGGOG00000005867	2 retrocopies	retro_ggor_525, retro_ggor_712,
Macropus eugenii	ENSMEUG00000011737	1 retrocopy	retro_meug_237,
Microcebus murinus	ENSMICG00000007377	1 retrocopy	retro_mmur_525,
Macaca mulatta	ENSMMUG00000003702	2 retrocopies	retro_mmul_1055, retro_mmul_2450,
Nomascus leucogenys	ENSNLEG00000006633	1 retrocopy	retro_nleu_2589,
Oryctolagus cuniculus	ENSOCUG00000005011	3 retrocopies	retro_ocun_392, retro_ocun_696, retro_ocun_763,
Otolemur garnettii	ENSOGAG00000010729	2 retrocopies	retro_ogar_2830, retro_ogar_943,
Ochotona princeps	ENSOPRG00000004170	1 retrocopy	retro_opri_498,
Pongo abelii	ENSPPYG00000014384	2 retrocopies	retro_pabe_596, retro_pabe_677,
Pan troglodytes	ENSPTRG00000015718	1 retrocopy	retro_ptro_437,
Rattus norvegicus	ENSRNOG00000001815	2 retrocopies	retro_rnor_1163 , retro_rnor_2340,
Rattus norvegicus	ENSRNOG00000030628	3 retrocopies	retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Ictidomys tridecemlineatus	ENSSTOG00000012601	1 retrocopy	retro_itri_858,
Tupaia belangeri	ENSTBEG00000002268	11 retrocopies	retro_tbel_114, retro_tbel_1488, retro_tbel_1500, retro_tbel_2048, retro_tbel_2524, retro_tbel_2729, retro_tbel_2733, retro_tbel_3159, retro_tbel_3793, retro_tbel_4599, retro_tbel_841,
Takifugu rubripes	ENSTRUG00000005660	2 retrocopies	retro_trub_14, retro_trub_6,
Tarsius syrichta	ENSTSYG00000013050	3 retrocopies	retro_tsyr_1905, retro_tsyr_903, retro_tsyr_935,