RetrogeneDB ID: retro_rnor_2911

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:36677475..36677987(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ppih
• Ensembl ID: ENSRNOG00000008489
• Aliases: Ppih, RGD1564921
• Description: None

Sequence

>retro_rnor_2911
GTGGCAAATTCTAGTCCAGTCAACCCTGTGTTTGTCTTTGATGTCAGCATTGGCAGCTAGGGAGTTGGTGGCATGAAGAT
CAAGCTGACTGCAGATGTGGTACCTAAGATTTACGAGAACTTTAGGTAATCCTTCACTGGAGAGTTCAGAAAGGATGGGT
TTCTGATAGGATACAAAATAAGCTCCTTCCACAGGATCATAAAGGAGTTTGTGATCCAGGGTGAAGATTTTCTTAATGGT
GAAGGTTCTGGGGTTGATGGTATTTATCAGGATCCGTTTACAGCTGAAAACTTATACGTAGACACTCAGGTCCACACATG
CTTTCCATGGTAAACAGTGGTTCCAAGACAAATAGGTGCCAGTTCTTCATCACATGTCCTAAGTGTGGTTGGCTCAGTAG
GAAGCATATAGTCATTGATGGGCTTCTAGTGATGTGAAAGATTGGGAATGTTCACACAGGCCTCAACAGTAAGCCCCAAA
CACCAGTGGTAATCTCACAGTGTGGAGAAATG

Alignment

ORF - retro_rnor_2911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.05 %
• Parental protein coverage: 98.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VANSSPVNPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDF
          VANSSPVNPV..FDVSIG...VG.MKI.L.ADVVPK..ENFR...TGEFRKDG..IGYK.S.FHR.IK.F
Retrocopy VANSSPVNPVFVFDVSIGS*GVGGMKIKLTADVVPKIYENFR*SFTGEFRKDGFLIGYKISSFHRIIKEF

Parental  MIQG-GFVNGDGTGVASIYRGPFADENFKL-RHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVF
          .IQG..F.NG.G.GV..IY..PF..EN....RHS.P..LSM.NSG..TN.CQFFITC.KC.WL..KH.V.
Retrocopy VIQGEDFLNGEGSGVDGIYQDPFTAENLYV<RHSGPHMLSMVNSGSKTNRCQFFITCPKCGWLSRKHIV-

Parental  GKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGEM
          ...IDGLLVM.KI.NV.TG.N.KP..PVVISQCGEM
Retrocopy ---IDGLLVM*KIGNVHTGLNSKPQTPVVISQCGEM

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	2.44 RPM
SRP017611_kidney	0.00 RPM	2.86 RPM
SRP017611_liver	0.00 RPM	1.68 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2911 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2911 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2911 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_3709
Rattus norvegicus	retro_rnor_2784

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003145	5 retrocopies	retro_cjac_129, retro_cjac_1886, retro_cjac_2205, retro_cjac_3120, retro_cjac_4110,
Macropus eugenii	ENSMEUG00000001691	1 retrocopy	retro_meug_1699,
Macaca mulatta	ENSMMUG00000013129	1 retrocopy	retro_mmul_1124,
Mustela putorius furo	ENSMPUG00000013966	2 retrocopies	retro_mputfur_285, retro_mputfur_542,
Mus musculus	ENSMUSG00000060288	7 retrocopies	retro_mmus_2563, retro_mmus_2873, retro_mmus_3195, retro_mmus_3709, retro_mmus_749, retro_mmus_913, retro_mmus_977,
Otolemur garnettii	ENSOGAG00000014937	1 retrocopy	retro_ogar_2368,
Procavia capensis	ENSPCAG00000011139	1 retrocopy	retro_pcap_81,
Rattus norvegicus	ENSRNOG00000008489	1 retrocopy	retro_rnor_2911 ,
Rattus norvegicus	ENSRNOG00000026900	2 retrocopies	retro_rnor_1216, retro_rnor_2392,