RetrogeneDB ID: retro_rnor_590

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:85035051..85036033(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pgk1
• Ensembl ID: ENSRNOG00000002467
• Aliases: Pgk1, Pgk
• Description: Phosphoglycerate kinase 1 [Source:UniProtKB/Swiss-Prot;Acc:P16617]

Sequence

>retro_rnor_590
ATGTCGCTTTCTAATAGGCTGACTTTGGATAAGCTGGATGTGAAGGGTAAGGGGGTCGTGATGAGGGTGAACTTCATTGT
TCCTATGAAGAACAACCAGATAACAAACAACCAAAGACTCAAGGCTGCTGTTCCAAGCATCAAATTCTGCTTGGACAGTG
GAGCCAATTCGGTTGTCCTTATGAACCACCTGGGCTGGCCTGATGGTGTTCCCATGCCTGACAAGAACTCTTTAGAGCCA
GTTGCTGCAGAACTCAAATCTCTGCTGGGCAAGGATGTTCTGTTCTTGAAGGATTGTGTGGGCCCAGAAGTAGAGAACGC
CTGTGCTAACCCAGCAGCTGGGACTGTCATTCTGCTGGAAAACCTCTGTTTTCATGTAGAGGAAGAAGGGAAGGGAAAAG
ATGCTTCTGTGAACAAGGTTAAAGCTGAGCCAGCCAAAATAGATGTTTTCTGAGCCTCCCTGTCCAAACTAGAAGATGTC
TATGTCAATTAGGCTTTTGGGACTGCACACCAAGCCCACATCTCCCTGGTGGGTATGAATCTGCTACAGAAGGCTGGTGG
ATTTTTGATGAAGAAGGAGCTGAACTACTTTGCCAAGGCTTTGGAGAGTCCAGAGTGAGCCTTCCTGGCTATCTTGGGAG
GAGCTAAAAAGTTGCAGACAAGATCCAGCTGATCAATAATATGCTAGACAAAGTCAATGAGATGATCCTTGGTGGTGGAA
TGGCTGTTACCTTCCTTAAGGTGCTCAATGAATGGAGATTGGCACATCTCTGTATGATGAAGGAGTTAAGATGGTCAAAG
ATTTCATGTCCAAAGCTGAGAAAAATGGCGTGAAGATTATCCTGCCTGTTGACTTTGTCACTGCTGACAAATTTGATGAG
CATGCCAAGACTGGCCAAGCTACTGTGGCCTCTGGTATACCTGCTGGCTGGATGGGCTTGGACTGTGGTACTGAGAGCAG
CAAGATATATGCTGAGGCTGTG

Alignment

ORF - retro_rnor_590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.92 %
• Parental protein coverage: 78.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGV
          MSLSN.LTLDKLDVKGK.VVMRV.F.VPMKNNQITNNQR.KAAVPSIKFCLD.GA.SVVLM.HLG.PDGV
Retrocopy MSLSNRLTLDKLDVKGKGVVMRVNFIVPMKNNQITNNQRLKAAVPSIKFCLDSGANSVVLMNHLGWPDGV

Parental  PMPDKYSLEPVAAELKSLLGKDVLFLKDCVGSEVENACANPAAGTVILLENLRFHVEEEGKGKDASGNKV
          PMPDK.SLEPVAAELKSLLGKDVLFLKDCVG.EVENACANPAAGTVILLENL.FHVEEEGKGKDAS.NKV
Retrocopy PMPDKNSLEPVAAELKSLLGKDVLFLKDCVGPEVENACANPAAGTVILLENLCFHVEEEGKGKDASVNKV

Parental  KAEPAKIDAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLA
          KAEPAKID.F.ASLSKL.DVYVN.AFGTAH.AH.S.VG.NL.QKAGGFLMKKELNYFAKALESPE..FLA
Retrocopy KAEPAKIDVF*ASLSKLEDVYVN*AFGTAHQAHISLVGMNLLQKAGGFLMKKELNYFAKALESPE*AFLA

Parental  I-LGGA-KVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNN-MEIGTSLYDEEGAKIVKDLMAKAEKNG
          I.LG...KVADKIQLINNMLDKVNEMI.GGGMA.TFLKVLN..MEIGTSLYDE.G.K.VKD.M.KAEKNG
Retrocopy I<LGRS*KVADKIQLINNMLDKVNEMILGGGMAVTFLKVLNE<MEIGTSLYDE-GVKMVKDFMSKAEKNG

Parental  VKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGTESSKKYAEAV
          VKI.LPVDFVTADKFDE.AKTGQATVASGIPAGWMGLDCGTESSK.YAEAV
Retrocopy VKIILPVDFVTADKFDEHAKTGQATVASGIPAGWMGLDCGTESSKIYAEAV

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	0.07 RPM	322.24 RPM
SRP017611_kidney	0.14 RPM	446.19 RPM
SRP017611_liver	0.00 RPM	184.97 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_590 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_590 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_590 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017619	1 retrocopy	retro_amel_117,
Bos taurus	ENSBTAG00000000894	1 retrocopy	retro_btau_1021,
Canis familiaris	ENSCAFG00000017270	2 retrocopies	retro_cfam_1194, retro_cfam_510,
Callithrix jacchus	ENSCJAG00000021082	3 retrocopies	retro_cjac_1367, retro_cjac_137, retro_cjac_4171,
Cavia porcellus	ENSCPOG00000023785	1 retrocopy	retro_cpor_102,
Equus caballus	ENSECAG00000014984	1 retrocopy	retro_ecab_557,
Felis catus	ENSFCAG00000013209	2 retrocopies	retro_fcat_123, retro_fcat_316,
Homo sapiens	ENSG00000102144	2 retrocopies	retro_hsap_1966, retro_hsap_90,
Gorilla gorilla	ENSGGOG00000017111	3 retrocopies	retro_ggor_1429, retro_ggor_2420, retro_ggor_3026,
Loxodonta africana	ENSLAFG00000011954	1 retrocopy	retro_lafr_13,
Macropus eugenii	ENSMEUG00000004779	3 retrocopies	retro_meug_11, retro_meug_1649, retro_meug_400,
Myotis lucifugus	ENSMLUG00000017791	2 retrocopies	retro_mluc_1657, retro_mluc_2159,
Macaca mulatta	ENSMMUG00000012874	1 retrocopy	retro_mmul_144,
Monodelphis domestica	ENSMODG00000004055	2 retrocopies	retro_mdom_140, retro_mdom_170,
Mus musculus	ENSMUSG00000062070	2 retrocopies	retro_mmus_29, retro_mmus_9,
Nomascus leucogenys	ENSNLEG00000001423	3 retrocopies	retro_nleu_2372, retro_nleu_2610, retro_nleu_79,
Oryctolagus cuniculus	ENSOCUG00000014726	1 retrocopy	retro_ocun_171,
Otolemur garnettii	ENSOGAG00000011104	1 retrocopy	retro_ogar_73,
Procavia capensis	ENSPCAG00000002117	1 retrocopy	retro_pcap_17,
Pongo abelii	ENSPPYG00000020496	3 retrocopies	retro_pabe_134, retro_pabe_1624, retro_pabe_3770,
Pan troglodytes	ENSPTRG00000022052	2 retrocopies	retro_ptro_2, retro_ptro_3229,
Rattus norvegicus	ENSRNOG00000002467	7 retrocopies	retro_rnor_1526, retro_rnor_1527, retro_rnor_2603, retro_rnor_3, retro_rnor_462, retro_rnor_590 , retro_rnor_611,
Sorex araneus	ENSSARG00000003956	1 retrocopy	retro_sara_14,
Sarcophilus harrisii	ENSSHAG00000001853	1 retrocopy	retro_shar_11,
Sus scrofa	ENSSSCG00000012440	1 retrocopy	retro_sscr_933,
Ictidomys tridecemlineatus	ENSSTOG00000001972	1 retrocopy	retro_itri_65,
Tupaia belangeri	ENSTBEG00000010309	1 retrocopy	retro_tbel_35,
Tarsius syrichta	ENSTSYG00000007917	1 retrocopy	retro_tsyr_40,
Vicugna pacos	ENSVPAG00000001208	1 retrocopy	retro_vpac_21,