RetrogeneDB ID: retro_rnor_204

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: AABR06110917.1:948..1215(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000049820
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Apoc1
• Ensembl ID: ENSRNOG00000018426
• Aliases: Apoc1, ALPCI, Apo-CIB, ApoC-IB, LRRG04
• Description: Apolipoprotein C-I Truncated apolipoprotein C-I [Source:UniProtKB/Swiss-Prot;Acc:P19939]

Sequence

>retro_rnor_204
ATGAGGCTCTTCATCGCTCTTCCTGTCCTGATTGTGGTCGTAGCCATGACCTTGGAAGGCCCAGCCCCCGCCCAGGCGGC
CCCGGATTTGTCCGGAACATTGGAGAGCATACCGGATAAACTGAAGGAGTTTGGGAACACTTTGGAAGACAAGGCCCGGG
CAGCCATTGAACATATCAAACAGAAGGAAATTTTGACCAAGACCCGGGCCTGGTTCTCAGAGGCATTTGGCAAAGTGAAG
GAGAAGTTGAAGACCACGTTCTCCTGA

Alignment

ORF - retro_rnor_204 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRLFIALPVLIVVVAMALEGPAPAQAAPDFSSAMESLPDKLKEFGNTLEDKARAAIEHIKQKEIMIKTRN
          MRLFIALPVLIVVVAM.LEGPAPAQAAPD.S...ES.PDKLKEFGNTLEDKARAAIEHIKQKEI..KTR.
Retrocopy MRLFIALPVLIVVVAMTLEGPAPAQAAPDLSGTLESIPDKLKEFGNTLEDKARAAIEHIKQKEILTKTRA

Parental  WFSETLNKMKEKLKTTFA
          WFSE...K.KEKLKTTF.
Retrocopy WFSEAFGKVKEKLKTTFS

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	2.44 RPM
SRP017611_kidney	0.00 RPM	0.42 RPM
SRP017611_liver	0.00 RPM	933.26 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_204 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_204 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
Ailuropoda melanoleuca	ENSAMEG00000012737	1 retrocopy	retro_amel_582,
Canis familiaris	ENSCAFG00000004615	1 retrocopy	retro_cfam_530,
Otolemur garnettii	ENSOGAG00000028159	1 retrocopy	retro_ogar_2801,
Rattus norvegicus	ENSRNOG00000018426	1 retrocopy	retro_rnor_204 ,
Tupaia belangeri	ENSTBEG00000007093	2 retrocopies	retro_tbel_1243, retro_tbel_2226,