RetrogeneDB ID: retro_rnor_963

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:61057286..61057683(-)
• Located in intron of: ENSRNOG00000011063

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gstm5
• Ensembl ID: ENSRNOG00000047034
• Aliases: None
• Description: Glutathione S-transferase Mu 5 [Source:UniProtKB/Swiss-Prot;Acc:Q9Z1B2]

Sequence

>retro_rnor_963
CCATGCTACTTCACAGATGAGATGAGGTTCCCCCAGAGTACTGCCATCTTGAGCTACCTCACTGCTCAGACAACATGCAT
GGTGATACTGAAGAAGAAAAGACAGAAGTGGACATCATGAAAAAGCGAATCATGGATTTCCATTCGCAACTTGTATGGCT
CTGCTACAGCGGGGGGGCTGAAAGTTTGAAGCCACCATGCTAGGAATAGCTACCTACATGACTTAAACAAACATCACTAC
TCCTGGGGAAATTCTCACAGTTTACAAGGGGAAAATTCACCTTTGTGGATTTCTCACTTAGGATATCTTAAGCCTGAACC
ATATGTTTGAGCCCAAGTTCCTGGATGAGTTCCCAAATCTGAAGGTTCTCATGGGCCTCTTTGGGGCTTTAGTGAAG

Alignment

ORF - retro_rnor_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.04 %
• Parental protein coverage: 59.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PYLMDGKNKITQSNAILRYIARK-HNMCGDTEEEKIRVDIMENQIMDFRMQLVRLCYNSNHESLKPQYLE
          P..........QS.AIL.Y......NM.GDTEEEK..VDIM...IMDF..QLV.LCY....ESLKP...E
Retrocopy PCYFTDEMRFPQSTAILSYLTAQ<DNMHGDTEEEKTEVDIMKKRIMDFHSQLVWLCYSGGAESLKPPC*E

Parental  QLPAQLKQFSLFLGKFTWFAGEKLTFVD-FLTYDVLDQNRMFEPKCLDEFPNLKAFMCRFEALEK
          .LP..LKQ.SL.LGKF..F...K.TFVD.FLT.D.L..N.MFEPK.LDEFPNLK..M..F.AL.K
Retrocopy *LPT*LKQTSLLLGKFSQFTRGKFTFVD<FLT*DILSLNHMFEPKFLDEFPNLKVLMGLFGALVK

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_963 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_963 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_491

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000018237	4 retrocopies	retro_rnor_2140, retro_rnor_2567, retro_rnor_2842, retro_rnor_769,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963 ,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,