RetrogeneDB ID: retro_rnor_2216

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:66559338..66559663(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pfdn6
• Ensembl ID: ENSRNOG00000000473
• Aliases: Pfdn6, Ke2
• Description: prefoldin 6 [Source:RefSeq peptide;Acc:NP_001158190]

Sequence

>retro_rnor_2216
ATGGCCGAACTGATCCAAAAGAAGGGAGAGGTAGAGAAATATCAACAGCTGCAGAAGGACTTGAGTAAATCCATGTCAGG
GAGGCAGAAGCTTGAATCCCAGCTAACGGAAAATAACATCGTGAAGGAGGAACTGGCCTTGCTGGATGGATCCAACGTGG
TCTTTAAGCTTCTGGGACCCGTGCTTGTCAAACAGGAGCTGGGGGAGGCTCGGGCCACAGTGGGGAATAGGCTAGACTAC
ATCACAGTGGAAATTAAGCGCTACGAATCGCAGCTTCGGGACCTCGAAAGGCAATCAGAGCAACAGAGGGGAAACCCTTG
CTCAG

Alignment

ORF - retro_rnor_2216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.59 %
• Parental protein coverage: 86.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG
          MAELIQKK..GEVEKYQQLQKDLSKSMSGRQKLE.QLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG
Retrocopy MAELIQKK--GEVEKYQQLQKDLSKSMSGRQKLESQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG

Parental  EARATVGKRLDYITAEIKRYESQLRDLERQSEQQR-ETLAQ
          EARATVG.RLDYIT.EIKRYESQLRDLERQSEQQR.ETLAQ
Retrocopy EARATVGNRLDYITVEIKRYESQLRDLERQSEQQR>ETLAQ

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	33.36 RPM
SRP017611_kidney	0.00 RPM	21.98 RPM
SRP017611_liver	0.07 RPM	11.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2216 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2216 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221, retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619,
Cavia porcellus	ENSCPOG00000019520	1 retrocopy	retro_cpor_570,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mus musculus	ENSMUSG00000024309	1 retrocopy	retro_mmus_1930,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Rattus norvegicus	ENSRNOG00000000473	2 retrocopies	retro_rnor_2216 , retro_rnor_2869,
Sorex araneus	ENSSARG00000006330	2 retrocopies	retro_sara_338, retro_sara_453,
Tupaia belangeri	ENSTBEG00000013280	1 retrocopy	retro_tbel_454,