RetrogeneDB ID: retro_rnor_1543

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:157399115..157399571(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pacrgl
• Ensembl ID: ENSRNOG00000004140
• Aliases: None
• Description: None

Sequence

>retro_rnor_1543
ATGTACAAATCAGACTGCCCTGGAGGTGTGCAGTTGAGAAACAGAGCAAGAGGTAGTTATGATCAATGGACACCCTGAAG
CACCCAAAGAAAACACAGGACTACAATTTAGGAGAGCAAATCCTCCTCGTTAGCCAGTTCTCTAGAGGCTACAAGAAGGG
CTCCGCCAGGGCAAGTGACAAACACCATCCCAAAACCATTAAGCTTTTCGGTGAACAGTCAAGAGCCCCTTCTGCATTCG
AAGCTCTTTACTCTCAAGGAGGCAATTCTTGCAGACTGCTACATGGCTCAATAAAACACAGATGACAGTGGGAGTGCCTG
CCTAAACTTCTTCCATTCGACCTGCTTCTAATTATGCTAGCCGAGGGTCTGAGGGAGAACAAGCCTCTTTTATACTTTGG
TGTTAAAAGAAGGATTTAGGAAGGTACTTCTTGTCAAGGGTGCTCCTGAAAAGGCC

Alignment

ORF - retro_rnor_1543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.13 %
• Parental protein coverage: 61.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQKSECSGGVQLRNRATGSNDR-TSSSTQVKHRTAVQRSKSSSLTSSPEAARRAHP-RPSDKLNPKTINP
          M.KS.C.GGVQLRNRA.GS.D..T..STQ.KHRT....SKSSSL.SS.EA.RRA.P.R.SDK..PKTI..
Retrocopy MYKSDCPGGVQLRNRARGSYDQWTP*STQRKHRTTI*ESKSSSLASSLEATRRAPP<RASDKHHPKTIKL

Parental  FGEQPRAPSAFAAIYSQGGIPCRLVHGSVKHRLQWECQPETLPFDPLLITLAEGLRETKHP-YTFVSKEG
          FGEQ.RAPSAF.A.YSQGG..CRL.HGS.KHR.QWEC.P..LPFD.LLI.LAEGLRE.K...YT.V.KEG
Retrocopy FGEQSRAPSAFEALYSQGGNSCRLLHGSIKHR*QWECLPKLLPFDLLLIMLAEGLRENKPL>YTLVLKEG

Parental  FRELLLVKDAPEKA
          FR..LLVK.APEKA
Retrocopy FRKVLLVKGAPEKA

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	3.95 RPM
SRP017611_kidney	0.00 RPM	1.54 RPM
SRP017611_liver	0.00 RPM	2.08 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1543 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1543 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1543 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015625	1 retrocopy	retro_dord_96,
Homo sapiens	ENSG00000163138	1 retrocopy	retro_hsap_488,
Gorilla gorilla	ENSGGOG00000012603	1 retrocopy	retro_ggor_458,
Macropus eugenii	ENSMEUG00000009937	2 retrocopies	retro_meug_1836, retro_meug_1954,
Monodelphis domestica	ENSMODG00000000641	2 retrocopies	retro_mdom_1541, retro_mdom_1646,
Oryctolagus cuniculus	ENSOCUG00000002186	1 retrocopy	retro_ocun_258,
Pan troglodytes	ENSPTRG00000015945	1 retrocopy	retro_ptro_368,
Rattus norvegicus	ENSRNOG00000004140	1 retrocopy	retro_rnor_1543 ,
Tarsius syrichta	ENSTSYG00000001584	1 retrocopy	retro_tsyr_1866,