RetrogeneDB ID: retro_rnor_2599

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:122325709..122325869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Crip1
• Ensembl ID: ENSRNOG00000027990
• Aliases: Crip1, Crip, Crp-1
• Description: Cysteine-rich protein 1 [Source:UniProtKB/Swiss-Prot;Acc:P63255]

Sequence

>retro_rnor_2599
GGCCGGGGCTGGCATCAGTGCTTCCTGGAGCGTGAAAATGCCGAAAGTCTCTCACCTCTGGGGACCATGAGGTCAAACCG
TACTGCAACCATCCCTTCTCCTCTGCCATGCTTGGCCCAAAGGCTTTGCCCAAGGAGCAGCTGAGCAGCACACTTTAAAG

Alignment

ORF - retro_rnor_2599 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.32 %
• Parental protein coverage: 74.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKDWHRPCLKCE-KCGKTLTSGGHAEHEGKPYCNHPCYSAMFG-PKGFGRGGAESHTFK
          G..WH...L..E.KC.K.LTSG....HE.KPYCNHP..SAM.G.PKGF..G.AE.HT.K
Retrocopy GRGWHQCFLERE<KCRKSLTSG---DHEVKPYCNHPFSSAMLG<PKGFAQGAAEQHTLK

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	2.23 RPM
SRP017611_kidney	0.00 RPM	4.95 RPM
SRP017611_liver	0.00 RPM	1.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2599 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2599 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2599 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047229	1 retrocopy	retro_btau_488,
Callithrix jacchus	ENSCJAG00000019788	1 retrocopy	retro_cjac_163,
Dipodomys ordii	ENSDORG00000001365	1 retrocopy	retro_dord_70,
Homo sapiens	ENSG00000213145	1 retrocopy	retro_hsap_2550,
Gorilla gorilla	ENSGGOG00000027381	1 retrocopy	retro_ggor_3,
Macropus eugenii	ENSMEUG00000001631	1 retrocopy	retro_meug_93,
Macaca mulatta	ENSMMUG00000007158	2 retrocopies	retro_mmul_1479, retro_mmul_553,
Pongo abelii	ENSPPYG00000006209	1 retrocopy	retro_pabe_114,
Pan troglodytes	ENSPTRG00000033768	1 retrocopy	retro_ptro_43,
Pteropus vampyrus	ENSPVAG00000014240	1 retrocopy	retro_pvam_1304,
Rattus norvegicus	ENSRNOG00000003772	1 retrocopy	retro_rnor_1763,
Rattus norvegicus	ENSRNOG00000005041	2 retrocopies	retro_rnor_141, retro_rnor_2541,
Rattus norvegicus	ENSRNOG00000027990	2 retrocopies	retro_rnor_2590, retro_rnor_2599 ,
Sarcophilus harrisii	ENSSHAG00000000807	1 retrocopy	retro_shar_341,
Tursiops truncatus	ENSTTRG00000004063	1 retrocopy	retro_ttru_1367,