RetrogeneDB ID: retro_rnor_1563

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:202480478..202481303(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pef1
• Ensembl ID: ENSRNOG00000013972
• Aliases: Pef1, Peflin
• Description: Peflin [Source:UniProtKB/Swiss-Prot;Acc:Q641Z8]

Sequence

>retro_rnor_1563
ATGCCTAGCTATCCAGACACGTAGAGTTGTCCAGGAGCTGCAGGACAGGTACCTGGACCACCCCAGGGGGCTCCTATCCT
GGACTTCCCCATGGTGGGCCAGTATGGAGGTGGATTCCCCCCTAGTGGTGGTTACAGAGCTCCTGCCCCTGGAGGACCCT
ATGGGTGCCCCGTGTTGGAGGAATCCCTTCTGGAACTCCAGGCGGACCATATGGCGGTGGACCACCAGGAGGTCCCAATG
GTCAGCTACCTCCAAGTCCCTATGGTACCCAGCAGCCTGGACCTTATGGACCGGGGTGTCCCCACCAACCCCCCAATGTG
GATCCTGAGGCCGACTCCTGGTTCCAGTCGGTGGATGCCAATGGCAGTGGCTATATCTCCCTCAAGGAGCTGAAGCTGGC
CCTGGTCAACTCCAACTGGTCCTCATGCAATGACGAGACAGGCCTCATGAGGATAAACGTGTTTTGACAAGACCGAGGCT
GGCCGCATTGATGCCGACATCTTCTCAGCCTTACGGAAATCCCTCCAGCCGTGGAGGAGCCTCTTTGAGCAGTGTGACCG
GGACCACTCGGGATCCATTCGCTCCACAGAGCTGCAGTAAGCGCTGTCCCAGATGGGCTACAACCTGAGCCCTCAGTTCA
CACAGCTCCCGGTTTCCCAATACTGCACGCGCTCTGCCATTCCCACCATGCAGCTGGACTGCTTCATCAAGGTGTGTGCC
CAGCTGCAGGTGTTGACTGAGGCCTTCCGCGAGGATACCACTGTACAGGGCAACATCCGGCTCAGCTCTGAGGACTTTGT
CGCCATGACAGCTTCAAGGATGCTA

Alignment

ORF - retro_rnor_1563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MASYPDGQSYPGAAGQVPGP-HPGGYYPGPPHGGGQY-GSGFPPGGYGAPAPGGPYG-YPSAGGTPSGTP
          M.SYPD..S.PGAAGQVPGP..PGG.YPG.PHGG....G...P.GGY.APAPGGPYG..P..GG.PSGTP
Retrocopy MPSYPDT*SCPGAAGQVPGP<TPGGSYPGLPHGGPVW>GGFPPSGGYRAPAPGGPYG<VPRVGGIPSGTP

Parental  GGPYGGGPPGGPYGGGPPGGPYGQAHPSPYGTQPPGPYGQGGVPPNVDPEAYSWFQSVDADHSGYISLKE
          GGPYGGGPPGGP.G..PP..PYG...P.PYG..P..P.....V.P....EA.SWFQSVDA..SGYISLKE
Retrocopy GGPYGGGPPGGPNGQLPP-SPYGTQQPGPYG--PGCPHQPPNVDP----EADSWFQSVDANGSGYISLKE

Parental  LKQALVNSNWSSFNDETCLMMINM-FDKTKTGRIDVVGFSALWKFLQQWKNLFQQYDRDHSGSISSTELQ
          LK.ALVNSNWSS.NDET.LM.IN..FDKT..GRID...FSAL.K.LQ.W..LF.Q.DRDHSGSI.STELQ
Retrocopy LKLALVNSNWSSCNDETGLMRINV>FDKTEAGRIDADIFSALRKSLQPWRSLFEQCDRDHSGSIRSTELQ

Parental  QALSQMGYNLSPQFTQLLVSRYCTRSAIPAMQLDCFIKVCTQLQVLTEAFREKDTAVQGNIRLSFEDFVT
          .ALSQMGYNLSPQFTQL.VS.YCTRSAIP.MQLDCFIKVC.QLQVLTEAFRE.DT.VQGNIRLS.EDFV.
Retrocopy *ALSQMGYNLSPQFTQLPVSQYCTRSAIPTMQLDCFIKVCAQLQVLTEAFRE-DTTVQGNIRLSSEDFVA

Parental  MTASRML
          MTASRML
Retrocopy MTASRML

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	29.62 RPM
SRP017611_kidney	0.00 RPM	41.80 RPM
SRP017611_liver	0.00 RPM	23.80 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1563 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1563 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1563 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006355	1 retrocopy	retro_cjac_1745,
Homo sapiens	ENSG00000162517	1 retrocopy	retro_hsap_497,
Gorilla gorilla	ENSGGOG00000015897	1 retrocopy	retro_ggor_464,
Macropus eugenii	ENSMEUG00000014458	1 retrocopy	retro_meug_375,
Microcebus murinus	ENSMICG00000001374	1 retrocopy	retro_mmur_937,
Macaca mulatta	ENSMMUG00000023397	1 retrocopy	retro_mmul_146,
Monodelphis domestica	ENSMODG00000017573	1 retrocopy	retro_mdom_1930,
Nomascus leucogenys	ENSNLEG00000001979	1 retrocopy	retro_nleu_2422,
Oryctolagus cuniculus	ENSOCUG00000005744	1 retrocopy	retro_ocun_461,
Pongo abelii	ENSPPYG00000001611	1 retrocopy	retro_pabe_238,
Pan troglodytes	ENSPTRG00000000463	1 retrocopy	retro_ptro_375,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563 , retro_rnor_2505,
Rattus norvegicus	ENSRNOG00000014485	1 retrocopy	retro_rnor_2840,
Rattus norvegicus	ENSRNOG00000049780	1 retrocopy	retro_rnor_1237,