RetrogeneDB ID: retro_cfam_540

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:7799121..7799835(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000684
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS7
• Ensembl ID: ENSCAFG00000004752
• Aliases: None
• Description: mitochondrial ribosomal protein S7 [Source:HGNC Symbol;Acc:14499]

Sequence

>retro_cfam_540
ATGGCGGCCCCCACGGTGAAGGCTGAGGGAGGCTGGCCGACCCTGGCGCTGAGCCTGCGGAGTGCCGTCCTGCGGCCTCC
GGGGCTAACCCACGTGAGCTGGAGCCGCCATGGTCCCGAATACAAGGATCCACGGATTGACCAGGAGTATTACCGTGAGC
CACTGGCAGAGTTGGCCGAGGAAGAGAAGTATGAACCGGAACTCAGGAAGACTCAGCTTACTTACCAAAGCTGCTCCAGC
AGCGAAAACAAGCTCTGTGTTTGAAGACCCCGTGGTCAGTAAACTCACCAACATGATGCTGAAAGGAGGAAACAAAGTCC
TGCCCAGATCCCTCCTGATGCAGACTCTGGAAGCTGTGAAACGGAAGCAGTTTGAGGAGTACCCTGCCGCTTCCGCAGAG
GAACAGGCCACCGTCGAAGGCAACCCCTATGCCGTCTTCCACCCAGCCTGCAGGGCTGTGAGCCCGTGATAGGGCTGGTG
CCCATCCTCAGAGGGGGCCATTTTTATCCGGTCCCTGTGCCACTTGCCCATCGGCGTCGTTGCTTCTTGGCCATGAAGTG
GATGATCAAGGAGTGCAGGGAGAAGAAGCACCGGCGGCTGCTGATGCCGGAGAAGTTGTCACACGAGCCGCTGGAGGCTT
TTCACACCGAGGGCCCTGTGATCAAGAAGAAGCGTGACATGCACAAGATGGCCGAGGCCAGCCGTGCCCTGGCT

Alignment

ORF - retro_cfam_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.83 %
• Parental protein coverage: 97.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAPAVKAAGGWPILALSLRSGVRRLPGLTQVRWSRYGPEYKDPRIDKEYYRKPLAELTEEEKYEQELRK
          MAAP.VKA.GGWP.LALSLRS.V.R.PGLT.V.WSR.GPEYKDPRID.EYYR.PLAEL.EEEKYE.ELRK
Retrocopy MAAPTVKAEGGWPTLALSLRSAVLRPPGLTHVSWSRHGPEYKDPRIDQEYYREPLAELAEEEKYEPELRK

Parental  TQ-LIKAAPAAKTSS-VFEDPVISKFTNMMMKGGNKVLARSLMMQTLEAVKRKQFEKYHAASAEEQATIE
          TQ.L...A..A...S.VFEDPV.SK.TNMM.KGGNKVL.RSL.MQTLEAVKRKQFE.Y.AASAEEQAT.E
Retrocopy TQ>LLTKAAPAAKTSSVFEDPVVSKLTNMMLKGGNKVLPRSLLMQTLEAVKRKQFEEYPAASAEEQATVE

Parental  RNPYVIFHQA-LQNCEPVIGLVPILRGGHFYQVPVPLADRRRRFLAMKWMIKECREKKHRRMLMPEKLSH
          .NPY..FH.A.LQ.CEPVIGLVPILRGGHFY.VPVPLA.RRR.FLAMKWMIKECREKKHRR.LMPEKLSH
Retrocopy GNPYAVFHPA<LQGCEPVIGLVPILRGGHFYPVPVPLAHRRRCFLAMKWMIKECREKKHRRLLMPEKLSH

Parental  ELLEAFHNQGPVIKKKHDMHKMAEANRALA
          E.LEAFH..GPVIKKK.DMHKMAEA.RALA
Retrocopy EPLEAFHTEGPVIKKKRDMHKMAEASRALA

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
SRP012049_cerebellum	0.00 RPM	32.21 RPM
SRP017611_brain	0.00 RPM	18.82 RPM
SRP017611_kidney	0.00 RPM	40.15 RPM
SRP017611_liver	0.00 RPM	11.67 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_540 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_540 has 0 orthologous retrocopies within eutheria group .

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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,