RetrogeneDB ID: retro_rnor_2185

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:160150103..160150445(+)
• Located in intron of: ENSRNOG00000014368

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD1307752
• Ensembl ID: ENSRNOG00000020317
• Aliases: None
• Description: RAB5-interacting protein [Source:RefSeq peptide;Acc:NP_001013944]

Sequence

>retro_rnor_2185
GCCAACCGGGCCCTCAAGGTGTCCGTGTGGAGCAAGGTGCTGCGGAGCGATGCAGGCTGGGATGACAAGGATGAATTTTT
AGATGTGATCTACTGGTTCCGACAGATCATCGCTGTGGTTTTGGGTGTCATTTGGGGCATTTTGCCCTTGCGAGGCTTCT
TGGGAATAGCAGGATTCTGCCTGATCAATGCAGGAGTCCTGTATCTCTACTTCAGCAACTACCTACAGATCGACGAGGAA
GAGTACAGTGGCACATGGGAGCTCACCAAAGACAGGTTTATGACGTCATTTGCCTTGTTCATGGTCATTTGGATCATCTT
TTACACTGCCATCCACCATGAC

Alignment

ORF - retro_rnor_2185 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 88.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANGALKVSVWSKVLRSDAAWDDKDEFLDVIYWFRQIIAVVLGVIWGILPLRGFLGIAGFCLINAGVLYLY
          AN.ALKVSVWSKVLRSDA.WDDKDEFLDVIYWFRQIIAVVLGVIWGILPLRGFLGIAGFCLINAGVLYLY
Retrocopy ANRALKVSVWSKVLRSDAGWDDKDEFLDVIYWFRQIIAVVLGVIWGILPLRGFLGIAGFCLINAGVLYLY

Parental  FSNYLQIDEEEYGGTWELTKEGFMTSFALFMVIWIIFYTAIHYD
          FSNYLQIDEEEY.GTWELTK..FMTSFALFMVIWIIFYTAIH.D
Retrocopy FSNYLQIDEEEYSGTWELTKDRFMTSFALFMVIWIIFYTAIHHD

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	0.07 RPM	29.41 RPM
SRP017611_kidney	0.28 RPM	53.94 RPM
SRP017611_liver	0.07 RPM	46.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2185 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2185 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2185 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021805	1 retrocopy	retro_btau_697,
Cavia porcellus	ENSCPOG00000011435	2 retrocopies	retro_cpor_1090, retro_cpor_1382,
Mustela putorius furo	ENSMPUG00000017777	1 retrocopy	retro_mputfur_1460,
Otolemur garnettii	ENSOGAG00000000891	1 retrocopy	retro_ogar_1796,
Rattus norvegicus	ENSRNOG00000020317	1 retrocopy	retro_rnor_2185 ,