RetrogeneDB ID: retro_rnor_2660

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:3785499..3785783(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Phf5a
• Ensembl ID: ENSRNOG00000024170
• Aliases: Phf5a, Ac2-246
• Description: PHD finger-like domain-containing protein 5A [Source:UniProtKB/Swiss-Prot;Acc:P83871]

Sequence

>retro_rnor_2660
TTCTGCTACAAGCAGGCTTGTGTAGCTTTCAGAAGACTGTGTGAAAAATAGGATGGCAAATGTGTGATCTGTGATTCCTA
TGTGTAGCCCTGCACCCTCGTTTGCATATGTGATGAGTGTGACTTTGGATCTAACCAGGCTGTTGTGTGATCATTGAAGG
TTCCGAATTCTTTGATGCCTACTCTTGTAAACAGTGTATCATTCTGGAGAAAGATAGAGATTGTTGCCCAAAATTTGTCA
ATTTGGGGAGCTCTAAGCGAGCCCTGTTCTATGAGCACAAACGA

Alignment

ORF - retro_rnor_2660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 86.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQ-GRCVICGGPGVSDAYYCKECTIQ
          FC.KQA.VA..RLCEK.DGKCVICDSYV.PCTLV.ICDEC..GS.Q.G.CVI..G....DAY.CK.C.I.
Retrocopy FCYKQACVAFRRLCEK*DGKCVICDSYV*PCTLVCICDECDFGSNQ<GCCVIIEGSEFFDAYSCKQCIIL

Parental  EKDRDGCPKIVNLGSSKTDLFYERKK
          EKDRD.CPK.VNLGSSK..LFYE.K.
Retrocopy EKDRDCCPKFVNLGSSKRALFYEHKR

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	12.65 RPM
SRP017611_kidney	0.00 RPM	20.66 RPM
SRP017611_liver	0.00 RPM	11.03 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2660 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2660 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015687	1 retrocopy	retro_amel_1674,
Canis familiaris	ENSCAFG00000001090	1 retrocopy	retro_cfam_369,
Callithrix jacchus	ENSCJAG00000004999	3 retrocopies	retro_cjac_1194, retro_cjac_1527, retro_cjac_906,
Echinops telfairi	ENSETEG00000010741	1 retrocopy	retro_etel_102,
Homo sapiens	ENSG00000100410	3 retrocopies	retro_hsap_2033, retro_hsap_2647, retro_hsap_2829,
Gorilla gorilla	ENSGGOG00000001104	2 retrocopies	retro_ggor_1848, retro_ggor_1965,
Latimeria chalumnae	ENSLACG00000012094	1 retrocopy	retro_lcha_25,
Microcebus murinus	ENSMICG00000013520	1 retrocopy	retro_mmur_758,
Macaca mulatta	ENSMMUG00000011354	3 retrocopies	retro_mmul_1390, retro_mmul_1471, retro_mmul_1503,
Mustela putorius furo	ENSMPUG00000016398	2 retrocopies	retro_mputfur_359, retro_mputfur_439,
Mus musculus	ENSMUSG00000061360	3 retrocopies	retro_mmus_1070, retro_mmus_1071, retro_mmus_1155,
Nomascus leucogenys	ENSNLEG00000015481	2 retrocopies	retro_nleu_1205, retro_nleu_653,
Oryctolagus cuniculus	ENSOCUG00000012705	1 retrocopy	retro_ocun_640,
Otolemur garnettii	ENSOGAG00000002839	1 retrocopy	retro_ogar_55,
Pongo abelii	ENSPPYG00000011870	2 retrocopies	retro_pabe_1661, retro_pabe_2324,
Pan troglodytes	ENSPTRG00000014427	3 retrocopies	retro_ptro_1352, retro_ptro_1917, retro_ptro_2479,
Pteropus vampyrus	ENSPVAG00000001162	1 retrocopy	retro_pvam_66,
Rattus norvegicus	ENSRNOG00000024170	3 retrocopies	retro_rnor_2660 , retro_rnor_2704, retro_rnor_2712,
Tarsius syrichta	ENSTSYG00000001082	1 retrocopy	retro_tsyr_259,
Tursiops truncatus	ENSTTRG00000003369	1 retrocopy	retro_ttru_1483,