RetrogeneDB ID: retro_rnor_488

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:153256787..153257556(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dnajc8
• Ensembl ID: ENSRNOG00000013255
• Aliases: None
• Description: DnaJ homolog subfamily C member 8 [Source:UniProtKB/Swiss-Prot;Acc:Q642C0]

Sequence

>retro_rnor_488
ATGGCAGCTTCGGGAGAGAGTGGTGCTTCTGGCGGAAGAGGCAGCACTGAAGAGGCATTTATGATCTGCTACAGTGAGAT
GAAACAAATACAGAATAGAGATTCAGTTCTAACATCCAAAAATCAGATTGAAAAATTGACTCGTCCTGGTTCCTATTACT
TTAATCTGAACCCATTTGAGGTTCATCAGATAGATCCAGAAGTGACAGATGAAAAAATAAAAAAGAGGTTTCGCCAGTTG
TTTATCTTGGTTCATCCTGACAAAAACCAAGATGATTCCAACACAGCACAGAAGACTTTTGAAGCTGTGGACACAGCTTA
CAGTTGCTACAGGATCAGGAATAAAAGAAGAGGGCCCTGGATGTAATTCAGGCAGGAAAAGATTATGTGGAACACACTGT
TAAAGAACAGGGGGAGGAGGGACAACTAAAGGAGGAAAGAAAGCCTACAAGTGTAGAGGAAGATGATCCCGAGCTGTTCA
AACAGGCAGTCTACAAACACACCATGAAGCTGTTTGCTGAGCTGCAGATTGAAAGGAAAGGGGGAGGAGCCAAAGAAATG
CATGAGAGGAAGTGCCAGAGAGAAGAGGCGATTTCAAGGCCAGGAAAAAGCCAAGCAAGAAAGAGAATGGCAGAAAAACG
TTGAGGAAAGTCAGGAGGGTTGAGTGGAGAGTTGACAAAATTTCCAGGCAAATAAATACAAATGGGAAGAATGAGAAGAA
GAATCAGACCTTCCTGCTGCCACTGAAAGTCAAGATGGAGAAACAGGAC

Alignment

ORF - retro_rnor_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.52 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAASGESGASGGGGSTEEAFMTFYSEVKQIEKRDSVLTSKNQIERLTRPGSSYFNLNPFEVLQIDPEVTD
          MAASGESGASGG.GSTEEAFM..YSE.KQI..RDSVLTSKNQIE.LTRPGS.YFNLNPFEV.QIDPEVTD
Retrocopy MAASGESGASGGRGSTEEAFMICYSEMKQIQNRDSVLTSKNQIEKLTRPGSYYFNLNPFEVHQIDPEVTD

Parental  EEIKKRFRQLSILVHPDKNQDDADRAQKAFEAVDKAY-KLLLDQEQKKRALDVIQAGKEYVEHTVKER--
          .....RFRQL.ILVHPDKNQDD...AQK.FEAVD.AY..LL.DQE.KKRALDVIQAGK.YVEHTVKE...
Retrocopy XXXXXRFRQLFILVHPDKNQDDSNTAQKTFEAVDTAY<QLLQDQE*KKRALDVIQAGKDYVEHTVKEQGE

Parental  KKQLKKEGKPTNVEEDDPELFKQAVYKQTMKLFAELEIKRKEREAKEMHERKRQREEEI-EAQEKAKRER
          ..QLK.E.KPT.VEEDDPELFKQAVYK.TMKLFAEL.I.RK...AKEMHERK.QREE.I...QEKAK.ER
Retrocopy EGQLKEERKPTSVEEDDPELFKQAVYKHTMKLFAELQIERKGGGAKEMHERKCQREEAI>QGQEKAKQER

Parental  EWQKNFEESRDGRVDSWRNFQAN-TKGKKEKK-NRTFLRPPKVKMEQRE
          EWQKN.EES..G.V.S..NFQAN.....K..K.N.TFL.P.KVKME...
Retrocopy EWQKNVEESQEG*VES*QNFQAN>NTNGKNEKKNQTFLLPLKVKMEKQD

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	56.15 RPM
SRP017611_kidney	0.00 RPM	43.75 RPM
SRP017611_liver	0.00 RPM	18.42 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_488 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_488 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011231	1 retrocopy	retro_amel_703,
Bos taurus	ENSBTAG00000018385	2 retrocopies	retro_btau_1332, retro_btau_794,
Canis familiaris	ENSCAFG00000011885	2 retrocopies	retro_cfam_1506, retro_cfam_1663,
Choloepus hoffmanni	ENSCHOG00000009649	1 retrocopy	retro_chof_1545,
Dasypus novemcinctus	ENSDNOG00000015452	2 retrocopies	retro_dnov_133, retro_dnov_914,
Erinaceus europaeus	ENSEEUG00000011136	2 retrocopies	retro_eeur_536, retro_eeur_638,
Echinops telfairi	ENSETEG00000008348	4 retrocopies	retro_etel_374, retro_etel_502, retro_etel_745, retro_etel_846,
Felis catus	ENSFCAG00000013393	1 retrocopy	retro_fcat_203,
Homo sapiens	ENSG00000126698	3 retrocopies	retro_hsap_1319, retro_hsap_2840, retro_hsap_4119,
Gorilla gorilla	ENSGGOG00000000821	2 retrocopies	retro_ggor_1030, retro_ggor_2766,
Microcebus murinus	ENSMICG00000001222	5 retrocopies	retro_mmur_1152, retro_mmur_1355, retro_mmur_343, retro_mmur_601, retro_mmur_935,
Macaca mulatta	ENSMMUG00000017080	4 retrocopies	retro_mmul_2004, retro_mmul_2078, retro_mmul_2168, retro_mmul_228,
Mustela putorius furo	ENSMPUG00000015540	1 retrocopy	retro_mputfur_202,
Mus musculus	ENSMUSG00000054405	1 retrocopy	retro_mmus_916,
Nomascus leucogenys	ENSNLEG00000009762	3 retrocopies	retro_nleu_1401, retro_nleu_1594, retro_nleu_2701,
Otolemur garnettii	ENSOGAG00000015597	4 retrocopies	retro_ogar_2422, retro_ogar_2595, retro_ogar_3219, retro_ogar_84,
Pongo abelii	ENSPPYG00000025833	2 retrocopies	retro_pabe_2351, retro_pabe_3382,
Pelodiscus sinensis	ENSPSIG00000017721	1 retrocopy	retro_psin_34,
Pteropus vampyrus	ENSPVAG00000017619	1 retrocopy	retro_pvam_1057,
Rattus norvegicus	ENSRNOG00000013255	1 retrocopy	retro_rnor_488 ,
Ictidomys tridecemlineatus	ENSSTOG00000012834	2 retrocopies	retro_itri_1361, retro_itri_1775,
Tarsius syrichta	ENSTSYG00000007057	3 retrocopies	retro_tsyr_137, retro_tsyr_1389, retro_tsyr_885,
Tursiops truncatus	ENSTTRG00000000047	1 retrocopy	retro_ttru_1430,