RetrogeneDB ID: retro_rnor_1938

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:165648052..165648445(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000008136
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RGD1563200
• Ensembl ID: ENSRNOG00000036830
• Aliases: None
• Description: None

Sequence

>retro_rnor_1938
ATGGAGCCAGAATCCATAGAAATTTGTCCTTATAACCCACACCACCGAATTCCTCTCAGCAGATTCCAGTACCACCTGGC
GTCGTGCAGAAAGAAGAACCCCAAGAAAGCCAAAAAGATGGCCAGCTGTAAATACAACGCCTGCCACGTGGTCCCCATCA
GAAAGCTGGCTGAACATGAAGCTACCTGTGTCAACAGAAGCTCCATGGAGGAAGAGGACGCCTTAGGCCCTCTGCAAGTC
AGCCTCCCACGGCCTCAGAACGAGGACACACTACAGGTCCGTTGGCTTTCCAGCCCTGATATTTGGAATGTTGACGGTGC
CAACTGTCACCCAATGTTCGTCCTTAAGAGTTTTGTTCCCCAAAAACTTGTTTGTGAAAGTGACATCCAAGAG

Alignment

ORF - retro_rnor_1938 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.39 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELESIELCPYDPNHRIPASRLQYHLASCKKKNPKIAKKMANCKYNACHVVPIKRLKEHEANCINRTAVD
          ME.ESIE.CPY.P.HRIP.SR.QYHLASC.KKNPK.AKKMA.CKYNACHVVPI..L.EHEA.C.NR....
Retrocopy MEPESIEICPYNPHHRIPLSRFQYHLASCRKKNPKKAKKMASCKYNACHVVPIRKLAEHEATCVNRSSME

Parental  -DEPLNLQKITQPSFEENENLCSAGSQFTDPDVWNVDHMNHFPSFVLETFAPKTLVCESDSRD
          ....L.......P....NE...........PD.WNVD..N..P.FVL..F.P..LVCESD...
Retrocopy EEDALGPLQVSLPR-PQNEDTLQV-RWLSSPDIWNVDGANCHPMFVLKSFVPQKLVCESDIQE

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	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1938 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1938 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_199

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000029590	1 retrocopy	retro_acar_141,
Ailuropoda melanoleuca	ENSAMEG00000000958	1 retrocopy	retro_amel_91,
Cavia porcellus	ENSCPOG00000023851	1 retrocopy	retro_cpor_93,
Felis catus	ENSFCAG00000031316	1 retrocopy	retro_fcat_1,
Mustela putorius furo	ENSMPUG00000005664	1 retrocopy	retro_mputfur_116,
Mus musculus	ENSMUSG00000053508	1 retrocopy	retro_mmus_199,
Rattus norvegicus	ENSRNOG00000036830	1 retrocopy	retro_rnor_1938 ,
Rattus norvegicus	ENSRNOG00000036831	1 retrocopy	retro_rnor_2525,