RetrogeneDB ID: retro_rnor_2889

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:4377756..4378429(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000047188
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pgam2
• Ensembl ID: ENSRNOG00000013532
• Aliases: Pgam2, D14Mgh1, PGAM-M, Pgmut
• Description: Phosphoglycerate mutase 2 [Source:UniProtKB/Swiss-Prot;Acc:P16290]

Sequence

>retro_rnor_2889
CTGAGCCCAGCAGGCTTCAAGGAGGCTAAACACAGCAGGCAGGCAATGCAAGATACTGGCTATGAGTTTGACATCTACTT
CACTTCTGTGCAGAAGAGAACAATCTGGACACTCTGGACAGTCCTGGATGCCACTGACCAGATGAGATTGCCAGTGGTCA
GGACTTGGTGCCTAGATGAGTGACACTATGGGGGTCTAATGGGTCTCAATAAAGCCAAAACTGCTGCTAAGCATGGTGAG
GCACAGGTAAAGATCTGGAGACAATCTTACAATGTTCCACCTCCTCCAATAGAGCCTGATAATCTATCCCTTCTACAGCA
ACATCAGCAAGGATTGCAGATATGCAGACATTGCTGAGTACCAGCTACCATGTGAGATCCTGAATGATACTATTGCTAGA
GTACTGCCCTTGTGGAATGAAAAAATTGTCCCCCAGATTAAGGAGGGAAAAAGGGTCTTGATTGTTGCCCATGGCAACAG
ACTTTGGGGCATTGTCAAAAATCTGGAGGGTCTCTCAGAAGAGGAAATCATGGAGCTGAACCTGCAAAGGGGTAGTCCCA
TTGTCTATGAATTGAACAAGAACTTGAAGCCCATCAAGTCCATGCAGTTCCTAGGAGATGAGGAGACTGTGCAGAAAGGC
ATGGAAGCTGTGCCTGCTTAGGGCAAGGTGAAA

Alignment

ORF - retro_rnor_2889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.16 %
• Parental protein coverage: 88.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSEKGAEEAKRGATAIKDAKIEFDICYTSVLKRAIRTLWTILDVTDQMWVPVVRTWRLNERHYGGLTGLN
          LS..G..EAK....A..D...EFDI..TSV.KR.I.TLWT.LD.TDQM..PVVRTW.L.E.HYGGL.GLN
Retrocopy LSPAGFKEAKHSRQAMQDTGYEFDIYFTSVQKRTIWTLWTVLDATDQMRLPVVRTWCLDE*HYGGLMGLN

Parental  KAETAAKHGEEQVKIWRRSFDTP-PPPMDEK-HNYYASISKDRRYAGLKPEELPTCESLKDTIARALPFW
          KA.TAAKHGE.QVKIWR.S...P.PP.........Y..ISKD.RYA......LP.CE.L.DTIAR.LP.W
Retrocopy KAKTAAKHGEAQVKIWRQSYNVPPPPIEPDN>YPFYSNISKDCRYADIAEYQLP-CEILNDTIARVLPLW

Parental  NEEIAPKIKAGKRVLIAAHGNSLRGIVKHLEGMSDQAIMELNLPTGIPIVYELNQELKPTKPMRFLGDEE
          NE.I.P.IK.GKRVLI.AHGN.L.GIVK.LEG.S...IMELNL..G.PIVYELN..LKP.K.M.FLGDEE
Retrocopy NEKIVPQIKEGKRVLIVAHGNRLWGIVKNLEGLSEEEIMELNLQRGSPIVYELNKNLKPIKSMQFLGDEE

Parental  TVRKAMEAVAAQGKAK
          TV.K.MEAV.A.GK.K
Retrocopy TVQKGMEAVPA*GKVK

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	3.95 RPM
SRP017611_kidney	0.00 RPM	3.49 RPM
SRP017611_liver	0.00 RPM	1.01 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2889 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2889 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024480	1 retrocopy	retro_dnov_34,
Macropus eugenii	ENSMEUG00000012920	8 retrocopies	retro_meug_1044, retro_meug_1303, retro_meug_1636, retro_meug_1838, retro_meug_202, retro_meug_2152, retro_meug_251, retro_meug_945,
Otolemur garnettii	ENSOGAG00000006713	1 retrocopy	retro_ogar_164,
Procavia capensis	ENSPCAG00000002181	1 retrocopy	retro_pcap_13,
Rattus norvegicus	ENSRNOG00000013532	1 retrocopy	retro_rnor_2889 ,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Tupaia belangeri	ENSTBEG00000004587	1 retrocopy	retro_tbel_3939,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,