RetrogeneDB ID: retro_rnor_1517

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:108094097..108094619(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam213a
• Ensembl ID: ENSRNOG00000011140
• Aliases: RGD1309676, Fam213a, PAMM
• Description: Redox-regulatory protein FAM213A [Source:UniProtKB/Swiss-Prot;Acc:Q6AXX6]

Sequence

>retro_rnor_1517
CAGGATCCAAGTTTCTTCACCATAGGTATGTGATCCATCGGTGCGGGAACCGTGGGGGCTCTGCTCCTGGCCAGCACAGA
CATATCTCTGTCCAAGACCCAGAAAGCGGCACTGGAATATTTGGAAGACATAGACATGAAAATACTGGAAAAATAACCAA
GGATATTCAAAGCAAAGGAGCTATGGGAAAAGAGTGGGGCTGTGATTATGGCTGGGCGAAGGCCAGGCTGCTTCCTCTGT
AGAACAGAGGCTGCAGACCTGTCATCCCTGAAGCCGATGCCAGATGCGGTAGGTGTTGTTCCCTATGTTGTGGTAAAGGT
GCAGATTAAGAGAGAAGCGAAGGACTTCCGGCCTTACTTCAAAGGGGAAATCTTCCTGGAGGAAAAGAAAAAAAAATTGT
ATGGTTCAGAGAGGCAGAAGATGATGTTCATGGGCTTCATTCGTTTGGGTGTGTGGTACAATTCCTTCCGGGCCTGGATT
AGAGGTTTCTCTGGAAACCTGGAAGGCGAAGGCTATATCCTC

Alignment

ORF - retro_rnor_1517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.79 %
• Parental protein coverage: 77.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDSSFFSMGMWSIGVGAFGAAALALLLANTDMFLSKPQKAALEYLEDIDLKTLEKEPRTFKAKELWEKNG
          QD.SFF..GM.SIG.G..G....ALLLA.TD..LSK.QKAALEYLEDID.K.LEK.PR.FKAKELWEK.G
Retrocopy QDPSFFTIGM*SIGAGTVG----ALLLASTDISLSKTQKAALEYLEDIDMKILEK*PRIFKAKELWEKSG

Parental  AVIMAVRRPGCFLCRAEAADLMSLKPKLDELGVPLYAVVKEKVKREVEDFQPYFKGEIFLD-EKKKFYGP
          AVIMA.RRPGCFLCR.EAADL.SLKP..D..GV..Y.VVK...KRE..DF.PYFKGEIFL.......YG.
Retrocopy AVIMAGRRPGCFLCRTEAADLSSLKPMPDAVGVVPYVVVKVQIKREAKDFRPYFKGEIFLEXXXXXLYGS

Parental  ERRKMMLMGLVRLGVWYNSFRAWKGGFSGNFEGEGFIL
          ER.KMM.MG..RLGVWYNSFRAW..GFSGN.EGEG.IL
Retrocopy ERQKMMFMGFIRLGVWYNSFRAWIRGFSGNLEGEGYIL

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	38.68 RPM
SRP017611_kidney	0.00 RPM	25.68 RPM
SRP017611_liver	0.00 RPM	40.34 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1517 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1517 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_2227

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000813	1 retrocopy	retro_chof_878,
Callithrix jacchus	ENSCJAG00000003657	1 retrocopy	retro_cjac_3312,
Dasypus novemcinctus	ENSDNOG00000001981	3 retrocopies	retro_dnov_1843, retro_dnov_1901, retro_dnov_868,
Homo sapiens	ENSG00000122378	2 retrocopies	retro_hsap_1135, retro_hsap_4076,
Gorilla gorilla	ENSGGOG00000013246	2 retrocopies	retro_ggor_2733, retro_ggor_886,
Microcebus murinus	ENSMICG00000007485	2 retrocopies	retro_mmur_1346, retro_mmur_1481,
Macaca mulatta	ENSMMUG00000021773	3 retrocopies	retro_mmul_2351, retro_mmul_2409, retro_mmul_881,
Mus musculus	ENSMUSG00000021792	1 retrocopy	retro_mmus_2227,
Otolemur garnettii	ENSOGAG00000013638	7 retrocopies	retro_ogar_2126, retro_ogar_2435, retro_ogar_2562, retro_ogar_3327, retro_ogar_420, retro_ogar_580, retro_ogar_784,
Procavia capensis	ENSPCAG00000009696	1 retrocopy	retro_pcap_281,
Pongo abelii	ENSPPYG00000025862	4 retrocopies	retro_pabe_3345, retro_pabe_643, retro_pabe_738, retro_pabe_944,
Pan troglodytes	ENSPTRG00000002685	2 retrocopies	retro_ptro_2763, retro_ptro_774,
Rattus norvegicus	ENSRNOG00000011140	1 retrocopy	retro_rnor_1517 ,