RetrogeneDB ID: retro_rnor_1127

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:87444195..87444628(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000024599
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rchy1
• Ensembl ID: ENSRNOG00000002546
• Aliases: None
• Description: RING finger and CHY zinc finger domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001007619]

Sequence

>retro_rnor_1127
CATTGCTTGAAATGTAACTTATGCCTAGTCATGAATCTTCGAGGAAAACACAAGTGTATTGAAAATGTTTCCTGGCAGAA
TTGTCCAATTTGCTTGGAGGACATTCACACCTCCTGTGTTGTTGTTCATGTCTTGCCTTGTGGGCATCTCCTAAATAGAA
TGTGTTATGAAGAAATGTTGAAAGAAGGTTACAGATGCCTTTTGTGTAAGCATTCTGCCTTAGACATGACTCGGTACTGG
AGACAATTAGATAATCAGGTAGCACCGACTCCTATGCCATCAGAATACCGGAACGTTACTGTTGATATTCTCTGCAATGA
TTGTACTGGACGATCCACAGTCCAGTTCCATATCTTAGTCATGAAATGTAAGCTTCGCGACTCCTACAATACTGCTCAAG
CTGGAAGGCCGCAGAGTTTCAGGGGTTCAACAG

Alignment

ORF - retro_rnor_1127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.52 %
• Parental protein coverage: 55.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HCLKCNLCLAMTLRGKHKCIENVSRQNCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCM
          HCLKCNLCL.M.LRGKHKCIENVS.QNCPICLEDIHTS.VV.HVLPCGHLL.R.CYEEMLKEGYRC.LC.
Retrocopy HCLKCNLCLVMNLRGKHKCIENVSWQNCPICLEDIHTSCVVVHVLPCGHLLNRMCYEEMLKEGYRCLLCK

Parental  HSALDMTRYWRQLDIEVAQTPMPSEYQNVTVDILCNDCNGRSTVQFHILGMKCKLCDSYNTAQAG-GRTV
          HSALDMTRYWRQLD..VA.TPMPSEY.NVTVDILCNDC.GRSTVQFHIL.MKCKL.DSYNTAQAG.GR.V
Retrocopy HSALDMTRYWRQLDNQVAPTPMPSEYRNVTVDILCNDCTGRSTVQFHILVMKCKLRDSYNTAQAG>GRRV

Parental  SMDEQ
          S...Q
Retrocopy SGVQQ

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	22.29 RPM
SRP017611_kidney	0.00 RPM	31.12 RPM
SRP017611_liver	0.00 RPM	13.58 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1127 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1127 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1127 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032536	1 retrocopy	retro_cfam_1449,
Choloepus hoffmanni	ENSCHOG00000011650	1 retrocopy	retro_chof_1142,
Macropus eugenii	ENSMEUG00000003266	1 retrocopy	retro_meug_1564,
Monodelphis domestica	ENSMODG00000019197	2 retrocopies	retro_mdom_314, retro_mdom_991,
Rattus norvegicus	ENSRNOG00000002546	2 retrocopies	retro_rnor_1127 , retro_rnor_607,
Tursiops truncatus	ENSTTRG00000013786	1 retrocopy	retro_ttru_1333,