RetrogeneDB ID: retro_rnor_1557

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:186955334..186955595(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ergic2
• Ensembl ID: ENSRNOG00000001852
• Aliases: None
• Description: endoplasmic reticulum-Golgi intermediate compartment protein 2 [Source:RefSeq peptide;Acc:NP_001020155]

Sequence

>retro_rnor_1557
ATGAGGCAACTGAATCGGAGAAAAACCTTAAGTTTGGTGAAAGAGTTAGATGCCTTTCCCAAGGTTCCTGACAGCTATGT
GGAGACATCAGCCAGTGGGGGAACAGTTTCTCTAATAGCATTTACCACTATGGCTTTATTAACAATAATGGAATTCTCAG
TGTATCAAGATACATGAAAGATGTATGAATATGAAGTAGACAAGGATTTTTCTAGCAAGTTGCGAATCAGCATACACATT
ACCATTGCCATGAAGTGTCAC

Alignment

ORF - retro_rnor_1557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.95 %
• Parental protein coverage: 79.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRRLNRRKTLSLVKELDAFPKVPDSYVETSASGGTVSLIAFTTMALLTIMEFSVYQDTWMKYEYEVDKDF
          MR.LNRRKTLSLVKELDAFPKVPDSYVETSASGGTVSLIAFTTMALLTIMEFSVYQDT...YEYEVDKDF
Retrocopy MRQLNRRKTLSLVKELDAFPKVPDSYVETSASGGTVSLIAFTTMALLTIMEFSVYQDT*KMYEYEVDKDF

Parental  SSKLRINIDITVAMKCH
          SSKLRI.I.IT.AMKCH
Retrocopy SSKLRISIHITIAMKCH

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	0.43 RPM	8.05 RPM
SRP017611_kidney	0.42 RPM	6.98 RPM
SRP017611_liver	0.27 RPM	5.24 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1557 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1557 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015668	1 retrocopy	retro_cpor_824,
Ornithorhynchus anatinus	ENSOANG00000010582	1 retrocopy	retro_oana_32,
Oryctolagus cuniculus	ENSOCUG00000017255	1 retrocopy	retro_ocun_1540,
Pongo abelii	ENSPPYG00000004390	1 retrocopy	retro_pabe_657,
Rattus norvegicus	ENSRNOG00000001852	1 retrocopy	retro_rnor_1557 ,
Sarcophilus harrisii	ENSSHAG00000004822	1 retrocopy	retro_shar_386,
Tupaia belangeri	ENSTBEG00000011223	1 retrocopy	retro_tbel_3783,