RetrogeneDB ID: retro_rnor_1353

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:47442906..47443334(+)
• Located in intron of: ENSRNOG00000017488

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufab1
• Ensembl ID: ENSRNOG00000018129
• Aliases: None
• Description: acyl carrier protein, mitochondrial [Source:RefSeq peptide;Acc:NP_001099764]

Sequence

>retro_rnor_1353
CTTTCTGCCCGTGTCTGCTCCTGCCCCAGCTTACCATACTGGCCTTGGCTGAAGCTCAGCCCCACTCTCTGCCCTGAGGG
AATGTGTAAGAGGCCCAGGACTCTGCATCCATCTTTGATGCTCTCTTGGGTTCTTGGAATGGTCACACACTTGTAGTGTT
AGGACAGTGACACACTCCATTTGACATTGGAGGAGATCAAGGACAAAGTGCTAAATGTCTAGAAACTCTATGACTAGGTT
GACCAAGAAAAGCGCTCAGTGAATTCTTGTTTTATGAAGGACCTAGGGTCAGGTGGTTTGGGCCAACCGGAGTTTATTTT
GGCTATGGGAGACAGCGTGGGGTTGAAATTCCTGATGGGGGTGCAGAGAAATTAATGTATCCACAAGAAACTGCAGAATA
CATTGCACGTAAGAAGAATGTGTATGAG

Alignment

ORF - retro_rnor_1353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.48 %
• Parental protein coverage: 92.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPAAFAPLPRLPTLALARPLSTILCPEGIWRRTGTLQPTLALAQVPGTVTHLCRQYSDAPPLTLEGIRDR
          L.A.....P.LP.......LS..LCPEG...R..TL.P.L.L..V.G.VTHL....SD...LTLE.I.D.
Retrocopy LSARVCSCPSLPYWPWLK-LSPTLCPEGMCKRPRTLHPSLMLSWVLGMVTHL*C*DSDTLHLTLEEIKDK

Parental  VLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGF-EIPDIDAEKLMCPQEIVDYIADK
          VL.V.KLYD..D.EK.SVNS.FMKDLG...L.Q.E.I.AM.D..G..EIPD..AEKLM.PQE...YIA.K
Retrocopy VLNV*KLYD*VDQEKRSVNSCFMKDLGSGGLGQPEFILAMGDSVGL<EIPDGGAEKLMYPQETAEYIARK

Parental  KDVYD
          K.VY.
Retrocopy KNVYE

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	0.07 RPM	37.75 RPM
SRP017611_kidney	0.00 RPM	70.41 RPM
SRP017611_liver	0.13 RPM	32.14 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1353 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1353 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1353 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_1724

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Choloepus hoffmanni	ENSCHOG00000003558	2 retrocopies	retro_chof_1517, retro_chof_2498,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635, retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728, retro_cpor_767,
Dasypus novemcinctus	ENSDNOG00000017122	5 retrocopies	retro_dnov_1450, retro_dnov_1733, retro_dnov_2024, retro_dnov_89, retro_dnov_911,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Homo sapiens	ENSG00000004779	1 retrocopy	retro_hsap_3484,
Gorilla gorilla	ENSGGOG00000006320	1 retrocopy	retro_ggor_2349,
Loxodonta africana	ENSLAFG00000001032	1 retrocopy	retro_lafr_330,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Microcebus murinus	ENSMICG00000007778	2 retrocopies	retro_mmur_1193, retro_mmur_120,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mustela putorius furo	ENSMPUG00000012142	2 retrocopies	retro_mputfur_1135, retro_mputfur_466,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Oryctolagus cuniculus	ENSOCUG00000008457	1 retrocopy	retro_ocun_1712,
Otolemur garnettii	ENSOGAG00000005562	2 retrocopies	retro_ogar_2916, retro_ogar_325,
Pongo abelii	ENSPPYG00000007192	1 retrocopy	retro_pabe_2879,
Pan troglodytes	ENSPTRG00000007889	1 retrocopy	retro_ptro_2358,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353 , retro_rnor_2058,
Sus scrofa	ENSSSCG00000010795	1 retrocopy	retro_sscr_1017,
Ictidomys tridecemlineatus	ENSSTOG00000024657	2 retrocopies	retro_itri_281, retro_itri_916,
Tursiops truncatus	ENSTTRG00000005258	2 retrocopies	retro_ttru_1229, retro_ttru_989,