RetrogeneDB ID: retro_fcat_1605

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D4:88160853..88161533(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000023481
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSME2
• Ensembl ID: ENSFCAG00000005585
• Aliases: None
• Description: proteasome (prosome, macropain) activator subunit 2 (PA28 beta) [Source:HGNC Symbol;Acc:9569]

Sequence

>retro_fcat_1605
ATGGCCAAGCCTTGTGGGGTGCGCCTGAGCGGGGAAGCCCGCAAACAGGTGGATATCTTCAGGCAAAATCTTTTTCAGGA
GGCAGAGGAATTCCTCTACAGATTCTTGCCCCAGAAAACCATATACCTGAATCAACTCTTGCAAGAGGACTCCCTCAATG
TGGCTGACCCGACCTCTCTCCGGGCCCCACTAGACATCCCCATCCCAGACGCCCCACCCAAGGATGATGAGATGGAAACA
GATAAGCAGGAGAAGAAAGAAGTCCCTAAGTGTGGCTTTCTCCCTGGAAATGAGAAGGTTCTCGCCCTACTTGCCCTGGT
TAAGCCAGAAGTGTGGACTCTCAGAGAAAAATGCATTCTGGTGATCACATGGATCCAGCACCTGATCCCCAAGATTGAGA
GGATGGAAATGACTTTGGGGTGGCAATCCAGGAGAAGGTGCTGGAGAGGGTGAATGCAGTCAAGACTAAAGTGGAAGCCT
TCCAAACAACCATTTCCAAGTACTTCTCAGAACGCGGGGATGCTGTGGCCAAGGCCTCTAAGGAGACTCAGGTCATGGAT
TACCGGGCCCTGGTACATCAGTGAGATGAAGCAGCCTATGGGGAGCTCAGGGCCATGGTGCTGGACCTGAGGGCCTTCTA
CGCTGAGCTTTATCATATCATCTGCAGCAACCTAGAGAAA

Alignment

ORF - retro_fcat_1605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.35 %
• Parental protein coverage: 94.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKPCGVRLSGEARKQVDIFRQNLFQEAEEFLYRFLPQKIIYLNQLLQEDSLNVADLTSLRAPLDIPIPD
          MAKPCGVRLSGEARKQVDIFRQNLFQEAEEFLYRFLPQK.IYLNQLLQEDSLNVAD.TSLRAPLDIPIPD
Retrocopy MAKPCGVRLSGEARKQVDIFRQNLFQEAEEFLYRFLPQKTIYLNQLLQEDSLNVADPTSLRAPLDIPIPD

Parental  PPPKDDEMETDKQEKKEVPKCGFLPGNEKVLALLALVKPEVWTLKEKCILVITWIQHLI-PKI-EDGNDF
          .PPKDDEMETDKQEKKEVPKCGFLPGNEKVLALLALVKPEVWTL.EKCILVITWIQHLI.P...EDGNDF
Retrocopy APPKDDEMETDKQEKKEVPKCGFLPGNEKVLALLALVKPEVWTLREKCILVITWIQHLI>PRL>EDGNDF

Parental  GVAIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYRALVHERDEAAYGELRAMVLD
          GVAIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKET.VMDYRALVH..DEAAYGELRAMVLD
Retrocopy GVAIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETQVMDYRALVHQ*DEAAYGELRAMVLD

Parental  LRAFYVSVEKLYCRTFIK
          LRAFY.......C....K
Retrocopy LRAFYAELYHIICSNLEK

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	0.34 RPM	8.95 RPM
SRP017611_kidney	1.03 RPM	19.58 RPM
SRP017611_liver	0.71 RPM	21.23 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1605 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1605 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007167	3 retrocopies	retro_cjac_233, retro_cjac_322, retro_cjac_71,
Felis catus	ENSFCAG00000005583	1 retrocopy	retro_fcat_1567,
Felis catus	ENSFCAG00000005585	1 retrocopy	retro_fcat_1605 ,
Myotis lucifugus	ENSMLUG00000009769	1 retrocopy	retro_mluc_2172,
Mus musculus	ENSMUSG00000079197	1 retrocopy	retro_mmus_145,
Otolemur garnettii	ENSOGAG00000016584	1 retrocopy	retro_ogar_61,
Sus scrofa	ENSSSCG00000002004	1 retrocopy	retro_sscr_302,