RetrogeneDB ID: retro_rnor_2128

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:19257685..19257898(+)
• Located in intron of: ENSRNOG00000008100

Retrocopy information

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

Parental gene information

• Parental gene symbol: Krtcap2
• Ensembl ID: ENSRNOG00000020542
• Aliases: None
• Description: Keratinocyte-associated protein 2 [Source:UniProtKB/Swiss-Prot;Acc:B2RZC9]

Sequence

>retro_rnor_2128
ATGCAGGTACCCACTTGCCAGTTGGTCTGTACCAAGTGGCTCACCTTTTAAGGTTAACTACTGGGCTCTGGCCTTTTCAT
CTTGTCCCTCGCAGCCTTCAGTAATCTGAACAATCTGGTCTTTGTTAAAGGTGTCCAAGCAAAGATCTTCCCTGAGACTC
TCCTCTGCTTGCTCTTGGTACTCATTGCATCCAGCCTCATCCACCAAGGATGC

Alignment

ORF - retro_rnor_2128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.61 %
• Parental protein coverage: 52.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQIYSRQLASTEWLTIQGGLLGSGLFVFSLTAFNNLENLVFGKGFQAKIFPEILLCLLLALFASGLIHRV
          MQ....QL..T.WLT..G.LLGSGLF..SL.AF.NL.NLVF.KG.QAKIFPE.LLCLLL.L.AS.LIH..
Retrocopy MQVPTCQLVCTKWLTF*G*LLGSGLFILSLAAFSNLNNLVFVKGVQAKIFPETLLCLLLVLIASSLIHQG

Parental  C
          C
Retrocopy C

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	18.41 RPM
SRP017611_kidney	0.00 RPM	20.10 RPM
SRP017611_liver	0.00 RPM	26.63 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2128 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2128 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2128 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011336	1 retrocopy	retro_amel_1789,
Canis familiaris	ENSCAFG00000017055	1 retrocopy	retro_cfam_1487,
Callithrix jacchus	ENSCJAG00000009017	1 retrocopy	retro_cjac_1289,
Felis catus	ENSFCAG00000025085	3 retrocopies	retro_fcat_1496, retro_fcat_477, retro_fcat_576,
Homo sapiens	ENSG00000163463	1 retrocopy	retro_hsap_2100,
Gorilla gorilla	ENSGGOG00000009303	1 retrocopy	retro_ggor_1635,
Macaca mulatta	ENSMMUG00000012180	2 retrocopies	retro_mmul_745, retro_mmul_987,
Mustela putorius furo	ENSMPUG00000005647	1 retrocopy	retro_mputfur_1653,
Nomascus leucogenys	ENSNLEG00000011864	1 retrocopy	retro_nleu_1306,
Oryctolagus cuniculus	ENSOCUG00000000347	1 retrocopy	retro_ocun_157,
Otolemur garnettii	ENSOGAG00000030271	1 retrocopy	retro_ogar_1306,
Pongo abelii	ENSPPYG00000000756	1 retrocopy	retro_pabe_1999,
Pan troglodytes	ENSPTRG00000001410	1 retrocopy	retro_ptro_1541,
Rattus norvegicus	ENSRNOG00000020542	1 retrocopy	retro_rnor_2128 ,
Ictidomys tridecemlineatus	ENSSTOG00000008829	1 retrocopy	retro_itri_1127,
Tarsius syrichta	ENSTSYG00000013228	2 retrocopies	retro_tsyr_1096, retro_tsyr_531,