RetrogeneDB ID: retro_rnor_214

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:32764499..32765507(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000017083
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Fam50a
• Ensembl ID: ENSRNOG00000045790
• Aliases: None
• Description: Protein Fam50a; Similar to XAP-5 protein (Predicted), isoform CRA_a [Source:UniProtKB/TrEMBL;Acc:G3V9M8]

Sequence

>retro_rnor_214
ATGGCGCAATACAAAGGTACCATGCGGGAGGCTGGCCGGGCCATGCATCTGATCAAGAAGCGCGAGAAGCAGAAGGAGCA
GATGGAGGTGCTGAAGCAACGCATTGCAGAGGAGACCATCATGAAGTCAAAAGTGGACAAGAAGTTCTCGGCACACTACG
ACGCTGTGGAAGCCGAGCTGAAGTCCAGCACGGTGGGCCTGGTGACCCTGAATGACATGAAGGCCAAGCAGGAGGCCCTG
CTGAGGGAGCGGGAGATACAGCTGGCCAAGAGGGAGCAACTGGAGCAGCGTCGGCTACAGCTAGAGATCCTGCGTGAGAA
GGAGCGAAGGCGCGAACGCAAGCGCAAGATCTCCAACCTGTCTTTCACGCTGGATGAGGAAGAAGACGGTGACCAAGAGG
ATGGCCGCCAGGCCGAAGGTGCTGAGGTCCACAGTGGTGGGGCCAAGAAGAACTTGGGCAAGAACCCCGATGTGGACACG
AGCTTCCTGCCCGATCGCGAACGCGAGGAGGAGGAGAACCGGCTGCGGGAGGAACTGCGGCAGGAGTGGGAGGCGAAGCG
CGAGAAGGTGAAGGGCGAGGAGGTGGAGATCACCTTCAGCTACTGGGATGGCTCTGGCCACCGGCGCACAGTACGCATGC
GCAAGGGCAGCACTGTGCAGCAGTTCCTGAAGCGGGCGCTGCAGGGGCTGCGCAGGGACTTCCGGGAGCTGCGGGCGGCG
GGCGTGGAGCAGCTCATGTACGTCAAGGAGGATCTCATCCTGCCGCACTACCACACCTTTTACGACTTCATCGTGGCCAA
AGCGCGGGGCAAGAGTGGGCCGCTCTTCAGCTTCGACGTGCACGATGATGTGCGGCTGCTGAGCGATGCCACGATGGAGA
AAGACGAGTCACACGCGGGAAAGGTGGTGCTGCGCAGCTGGTATGAGAAGAACAAGCACATCTTCCCCGCCAGCCGCTGG
GAGCCCTACGACCCCGAGAAGAAGTGGGACAAGTACACCATCCGGTGA

Alignment

ORF - retro_rnor_214 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.17 %
• Parental protein coverage: 55.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKKLGKNPDVDTSFLPDRDREEEENRLREELRQEWEAKQEKIKSEEIEITFSYWDGSGHRRTVKMKKGNT
          KK.LGKNPDVDTSFLPDR.REEEENRLREELRQEWEAK.EK.K.EE.EITFSYWDGSGHRRTV.M.KG.T
Retrocopy KKNLGKNPDVDTSFLPDREREEEENRLREELRQEWEAKREKVKGEEVEITFSYWDGSGHRRTVRMRKGST

Parental  MQQFLQKALEILRKDFSELRSAGVEQLMYIKEDLIIPHHHSFYDFIVTKARGKSGPLFNFDVHDDVRLLS
          .QQFL..AL..LR.DF.ELR.AGVEQLMY.KEDLI.PH.H.FYDFIV.KARGKSGPLF.FDVHDDVRLLS
Retrocopy VQQFLKRALQGLRRDFRELRAAGVEQLMYVKEDLILPHYHTFYDFIVAKARGKSGPLFSFDVHDDVRLLS

Parental  DATVEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR
          DAT.EKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR
Retrocopy DATMEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR

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	0.07 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_214 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_214 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_214 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000273	1 retrocopy	retro_amel_15,
Felis catus	ENSFCAG00000011399	1 retrocopy	retro_fcat_100,
Homo sapiens	ENSG00000071859	1 retrocopy	retro_hsap_94,
Loxodonta africana	ENSLAFG00000008766	1 retrocopy	retro_lafr_43,
Myotis lucifugus	ENSMLUG00000022234	1 retrocopy	retro_mluc_7,
Mustela putorius furo	ENSMPUG00000009476	1 retrocopy	retro_mputfur_145,
Mus musculus	ENSMUSG00000001962	1 retrocopy	retro_mmus_103,
Nomascus leucogenys	ENSNLEG00000014266	1 retrocopy	retro_nleu_109,
Rattus norvegicus	ENSRNOG00000045790	1 retrocopy	retro_rnor_214 ,
Sorex araneus	ENSSARG00000006465	1 retrocopy	retro_sara_554,
Sus scrofa	ENSSSCG00000025303	1 retrocopy	retro_sscr_56,
Ictidomys tridecemlineatus	ENSSTOG00000004448	10 retrocopies	retro_itri_105, retro_itri_1563, retro_itri_1688, retro_itri_1691, retro_itri_1693, retro_itri_1758, retro_itri_1760, retro_itri_1762, retro_itri_1780, retro_itri_184,