RetrogeneDB ID: retro_rnor_1176

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:8736182..8736604(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmem160
• Ensembl ID: ENSRNOG00000015304
• Aliases: Tmem160, RGD1564549
• Description: transmembrane protein 160 precursor [Source:RefSeq peptide;Acc:NP_001099697]

Sequence

>retro_rnor_1176
TTCTGTAAAGGCCATCCTGTGACCTCAGTGGCCCCACGGCACTCTGAGCTGGATCACGAGGACGTTTAGCTCCTCTGCAA
GGCACATGAGACAGCTTTCCTCTCCTCGTCCTGAAACGGACTTCTGGCATCAGGCACTGGGGTCACCTCCTTCATGCAGA
GTGACATAGACTGGGAAGCTGCCTATGGCTTCTCCTTGCTGGGTGGCCTGTGCATGGTGTGGGGCGGACCTCCTATGCAG
ACTGCCAGGGACCCAGGCAACTGTGGCTTGCAGGTCCTGGCACTGGTGTGTGGGCAGAATTGGCTGCCAGTTTGCTCTGG
CCTTGAACTGAAGGCCTCTACAAGGACCAGTTGGAACTGGACACGGAATTGGTGCGTGAGGACGATGAGGCAGCCAGGAC
AGAAGGCCCAGATGAAGGAGGG

Alignment

ORF - retro_rnor_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.51 %
• Parental protein coverage: 78.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FAPGHGPRAGASPPPVSELDRADAWLLRKAHETAFLSWFRNGLLASGIGVISFMQSDMGREAAYGFFLLG
          F..GH.....A..P..SELD..D..LL.KAHETAFLS...NGLLASG.GV.SFMQSD...EAAYGF.LLG
Retrocopy FCKGHPVTSVA--PRHSELDHEDV*LLCKAHETAFLSSS*NGLLASGTGVTSFMQSDIDWEAAYGFSLLG

Parental  GLCVVW-GGASYAVGLAALRGPMQLSLAGAAAGVGAVLAASLLWACAVGLYMGQLELDVELVPEDDGAAS
          GLC.VW.G..SY....A...GP.QL.LAG...GV.A.LAASLLW....GLY..QLELD.ELV.EDD.AA.
Retrocopy GLCMVW<GRTSY----ADCQGPRQLWLAGPGTGVWAELAASLLWP*TEGLYKDQLELDTELVREDDEAAR

Parental  TEGPDEAG
          TEGPDE.G
Retrocopy TEGPDEGG

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	17.97 RPM
SRP017611_kidney	0.00 RPM	11.03 RPM
SRP017611_liver	0.00 RPM	10.89 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1176 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1176 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000017997	1 retrocopy	retro_etel_2100,
Homo sapiens	ENSG00000130748	1 retrocopy	retro_hsap_1828,
Gorilla gorilla	ENSGGOG00000013410	1 retrocopy	retro_ggor_2165,
Oryctolagus cuniculus	ENSOCUG00000023097	1 retrocopy	retro_ocun_1750,
Pongo abelii	ENSPPYG00000010166	1 retrocopy	retro_pabe_1498,
Pan troglodytes	ENSPTRG00000011200	1 retrocopy	retro_ptro_1165,
Rattus norvegicus	ENSRNOG00000015304	1 retrocopy	retro_rnor_1176 ,