RetrogeneDB ID: retro_rnor_484

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:148620092..148620341(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000046626
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MGC105649
• Ensembl ID: ENSRNOG00000050251
• Aliases: MGC105649, Nmes1
• Description: rno-mir-147 [Source:miRBase;Acc:MI0006130]

Sequence

>retro_rnor_484
ATGGGCATTTTCCAGAGATTGATGAAAAATAAGGAACTCATTCCTTTGGCGTTTTTTATAAGCGTGGCTGCCACTGGAGC
CTCACCTTTCGCTTTGTATGCTTTGAAAAAAACTGACGTGGTTATTAATCGAAAAAGAAACCCAGAACCTTGGGAAATGG
TGGATCTTACTCAACCCCAAAAGCTTATAACCATCAACCAGCAATGGAAGCCCATTGAGTTGCTGCAGAAAGTCCGGAGA
GCAACCAGA

Alignment

ORF - retro_rnor_484 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGIFQRLMKNKELIPLAFFISAAATGASSFALYALKKTDVVIDRKRDPEPWETVDPTQPQKLLTINQEWK
          MGIFQRLMKNKELIPLAFFIS.AATGAS.FALYALKKTDVVI.RKR.PEPWE.VD.TQPQKL.TINQ.WK
Retrocopy MGIFQRLMKNKELIPLAFFISVAATGASPFALYALKKTDVVINRKRNPEPWEMVDLTQPQKLITINQQWK

Parental  PVEELQRVRRATR
          P.E.LQ.VRRATR
Retrocopy PIELLQKVRRATR

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	0.07 RPM
SRP017611_kidney	0.00 RPM	1.47 RPM
SRP017611_liver	0.00 RPM	0.20 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_484 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_484 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_484 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031501	2 retrocopies	retro_cfam_1654, retro_cfam_669,
Cavia porcellus	ENSCPOG00000020706	1 retrocopy	retro_cpor_450,
Erinaceus europaeus	ENSEEUG00000003556	1 retrocopy	retro_eeur_594,
Macropus eugenii	ENSMEUG00000013137	4 retrocopies	retro_meug_1593, retro_meug_2033, retro_meug_278, retro_meug_63,
Monodelphis domestica	ENSMODG00000028279	1 retrocopy	retro_mdom_225,
Oryctolagus cuniculus	ENSOCUG00000029216	1 retrocopy	retro_ocun_33,
Rattus norvegicus	ENSRNOG00000050251	1 retrocopy	retro_rnor_484 ,
Sarcophilus harrisii	ENSSHAG00000006433	3 retrocopies	retro_shar_296, retro_shar_416, retro_shar_744,
Ictidomys tridecemlineatus	ENSSTOG00000021929	1 retrocopy	retro_itri_1133,