RetrogeneDB ID: retro_fcat_2013

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:98178454..98178978(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000028730
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS7
• Ensembl ID: ENSFCAG00000028759
• Aliases: None
• Description: mitochondrial ribosomal protein S7 [Source:HGNC Symbol;Acc:14499]

Sequence

>retro_fcat_2013
AAGTATGAGTAGGAACTCAGGAAGACTCAGCTTATCAAAGCTGCCCCAGCGATGAAAACAAGCTCTGTGTTTGAAGACCC
AGTGATCAGCAAATCCTCCAACATGATGATGAAAGGCAGAAACAAAGTACTGGCCACATCCTTCATGATGCAGACTCTGG
AAGCTGTGAAAGGAAGCATTTTGAGAAGTACCATGCTTCTGCAGAACAGGCAGCCATCAAACGCAACCCCTACAACATCT
TCCACCAAGCACTGGAGAACTGTGAGCCTGTGGTTGGGCTGGTACCCATCCTCAGAGGTGGCCATTTCTACCAGGTCCCT
GTGCCACTGGCTGACTGGCGTCGCCACTTCCTGGCCATGAAGTGGATGATTACTGAGTGCAGGGAGAAGCACTGGAGGAT
GCTGACGCCAGAGAGGTCATCACATGAGCTGCTGGAGGCTTTTCACAACCAGGGCACTATGATCAAGAAGTATGACATGA
ACAAGATGACTGAGGCCATCCATGCCCTAGCTCACTACTGCTGG

Alignment

ORF - retro_fcat_2013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.33 %
• Parental protein coverage: 73.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KYERELRKTQHIKAAPASKTSSVFEDPVISKFTNMIMKGGNKVLARSLMAQTLEAVK-RKQFEKYHAASA
          KYE.ELRKTQ.IKAAPA.KTSSVFEDPVISK..NM.MKG.NKVLA.S.M.QTLEAVK.RK.FEKYHA...
Retrocopy KYE*ELRKTQLIKAAPAMKTSSVFEDPVISKSSNMMMKGRNKVLATSFMMQTLEAVK<RKHFEKYHASA-

Parental  EERASIERNPYTIFHQALKNCEPVIGLVPILRGGHFYQVPVPLADRRRRFLAMKWMITECREKKHRRVLM
          .E.A.I.RNPY.IFHQAL.NCEPV.GLVPILRGGHFYQVPVPLAD.RR.FLAMKWMITECRE.KH.R.L.
Retrocopy -EQAAIKRNPYNIFHQALENCEPVVGLVPILRGGHFYQVPVPLADWRRHFLAMKWMITECRE-KHWRMLT

Parental  PEKLSHELLEAFHNQGPVIKKKHDMHKMAEANRALAHYRW
          PE..SHELLEAFHNQG..I.KK.DM.KM.EA..ALAHY.W
Retrocopy PERSSHELLEAFHNQGTMI-KKYDMNKMTEAIHALAHYCW

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	35.35 RPM
SRP017611_kidney	0.00 RPM	52.77 RPM
SRP017611_liver	0.00 RPM	24.26 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_2013 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_2013 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009287	1 retrocopy	retro_amel_1444,
Canis familiaris	ENSCAFG00000004752	5 retrocopies	retro_cfam_2020, retro_cfam_2197, retro_cfam_438, retro_cfam_443, retro_cfam_540,
Callithrix jacchus	ENSCJAG00000014458	2 retrocopies	retro_cjac_290, retro_cjac_3316,
Erinaceus europaeus	ENSEEUG00000015775	1 retrocopy	retro_eeur_212,
Felis catus	ENSFCAG00000028759	2 retrocopies	retro_fcat_2013 , retro_fcat_424,
Loxodonta africana	ENSLAFG00000002873	1 retrocopy	retro_lafr_945,
Macropus eugenii	ENSMEUG00000012264	1 retrocopy	retro_meug_1826,
Mustela putorius furo	ENSMPUG00000013928	1 retrocopy	retro_mputfur_976,
Oryctolagus cuniculus	ENSOCUG00000017928	1 retrocopy	retro_ocun_609,
Procavia capensis	ENSPCAG00000015942	1 retrocopy	retro_pcap_327,
Pteropus vampyrus	ENSPVAG00000008433	3 retrocopies	retro_pvam_610, retro_pvam_615, retro_pvam_678,
Ictidomys tridecemlineatus	ENSSTOG00000015200	2 retrocopies	retro_itri_1805, retro_itri_461,