RetrogeneDB ID: retro_rnor_623

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:181260690..181261166(-)
• Located in intron of: ENSRNOG00000013934

Retrocopy information

• Ensembl ID: ENSRNOG00000038673
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RGD1566265
• Ensembl ID: ENSRNOG00000002323
• Aliases: None
• Description: None

Sequence

>retro_rnor_623
CAGAAGGGCAACATGAAAGTTGCCAGGATACATGCTGAAAATTCCATCCGCCAGAAGAATCAAGTGGTGAACTTCTTGAG
AATGAGTGCACGAGTGGGTGCAGTGGCTGCCAGAGTCCAGACTGCAGTGAAAATGGTTAAAGTGACCAAATCCATGGCTG
ATGTGGTTAAGTCAGTGGACGCGATGTTGAAAACTGTGAATCTGGAAAAGATCTCTGCTTTGATGGACAAATTCCAACAC
CAGTTTGAGACCCTGGACGTCCAGACACAGCAAATGGAAGACACCATGAGCAGCATGACGACGCTAACCACTCCCCAGAA
CCAAGTGGATGTGCCCTCCAGGAAATGGCAGATGAGGTAGACCTCGATCTCAATGTAGAGCTGACTCAGGGCCAGGCCCG
TTCCATGGGAACAAGCATGGCTTCCGTTGAGCAAGATGAACTGCCCCAGAGACTGGCCCTCCTTTGGGATCAAGTG

Alignment

ORF - retro_rnor_623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 79.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKGNTEVARIHAENAIRQKNQAINFLRMSARVDAVAARVQTAVTMGKVTKSMAGVVKSMDATLRSMNLEK
          QKGN..VARIHAEN.IRQKNQ..NFLRMSARV.AVAARVQTAV.M.KVTKSMA.VVKS.DA.L...NLEK
Retrocopy QKGNMKVARIHAENSIRQKNQVVNFLRMSARVGAVAARVQTAVKMVKVTKSMADVVKSVDAMLKTVNLEK

Parental  ISALMDKFEHQFETLDVQTQQMEDTMSSTTTLTTPQNQVDM-LLQEMADEAGLDLNMELPQGQTGSVGAS
          ISALMDKF.HQFETLDVQTQQMEDTMSS.TTLTTPQNQVD...LQEMADE..LDLN.EL.QGQ..S.G.S
Retrocopy ISALMDKFQHQFETLDVQTQQMEDTMSSMTTLTTPQNQVDV<ALQEMADEVDLDLNVELTQGQARSMGTS

Parental  VASTEQDELSQRLARLRDQV
          .AS.EQDEL.QRLA.L.DQV
Retrocopy MASVEQDELPQRLALLWDQV

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	15.96 RPM
SRP017611_kidney	0.00 RPM	5.51 RPM
SRP017611_liver	0.00 RPM	4.71 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_623 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_623 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_623 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000026660	1 retrocopy	retro_cpor_1434,
Equus caballus	ENSECAG00000018625	1 retrocopy	retro_ecab_991,
Gorilla gorilla	ENSGGOG00000025604	1 retrocopy	retro_ggor_1368,
Loxodonta africana	ENSLAFG00000026457	2 retrocopies	retro_lafr_214, retro_lafr_826,
Macropus eugenii	ENSMEUG00000015250	2 retrocopies	retro_meug_1196, retro_meug_205,
Myotis lucifugus	ENSMLUG00000024811	3 retrocopies	retro_mluc_1161, retro_mluc_1344, retro_mluc_673,
Monodelphis domestica	ENSMODG00000004273	2 retrocopies	retro_mdom_1444, retro_mdom_154,
Mus musculus	ENSMUSG00000031242	1 retrocopy	retro_mmus_1735,
Ochotona princeps	ENSOPRG00000018556	1 retrocopy	retro_opri_577,
Pongo abelii	ENSPPYG00000020505	1 retrocopy	retro_pabe_1581,
Pteropus vampyrus	ENSPVAG00000001416	2 retrocopies	retro_pvam_208, retro_pvam_59,
Rattus norvegicus	ENSRNOG00000002323	2 retrocopies	retro_rnor_1361, retro_rnor_623 ,
Sarcophilus harrisii	ENSSHAG00000016903	2 retrocopies	retro_shar_776, retro_shar_778,
Tarsius syrichta	ENSTSYG00000011727	1 retrocopy	retro_tsyr_1611,
Tursiops truncatus	ENSTTRG00000008066	2 retrocopies	retro_ttru_1002, retro_ttru_235,
Vicugna pacos	ENSVPAG00000000854	2 retrocopies	retro_vpac_112, retro_vpac_422,