RetrogeneDB ID: retro_cfam_438

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:667643..668300(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000023945
• 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_438
CTGTCCTGCGGCTTCCGGGCTAGCCCGGGGAGGTGGAGCCGCCGTGGTCCCGAATCCAAGGGTCCACGGATCGACCGGGA
GTATTACCGGAAGCCATTGGCAGAGTTGGCTGAGCAAGAGAAGTATGAACCGGAACTCAGGAAGACTCAGCTTATCAAAG
CTGCTCCAGCAGCGAAAACAAGCTCTGGGTGTGAAGACCCCGTGATCAGTAAATTCACCGACATGATGATGAAAGGAGGA
AACGGAGTACTGGCCAGATCCCTCCTGGTGCAGACTCGAAGCTGTGAAAAGGAAGCAGTTTGAGAAGTACCACGCTGCTT
CTGCAGAGGAACAGGCCTCCAGGGAACGCAACCGCCGTGCCGTCTCCCACCCAGCCTGCAGAGCTGCGAGCCCGTGATAG
GGCTGGTGCCCATCCTCAGAGGGGGCCGTTTTTATCAGGGCCCTGTGCCACTTGCCCGTCGGCGGCGTCGCTTCTTGGCC
ATGAAGTGGATGATTAAGGAGTGCAGGGAGAAGAAGCACCGGCGGATGCTGATGCCGGAGAAGTTGTCACACGAGCCACT
GGAGGCTTTTCACAACCAGGGCCCTGTGATCAAGAAGAAGCGCGACATGCACAAGACGGCCGAGGCCAGCCGCGCCCGGG
CCCGCTGCCGCAGGTGG

Alignment

ORF - retro_cfam_438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.93 %
• Parental protein coverage: 92.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRSGVRRLPGLTQVRWSRYGPEYKDPRIDKEYYRKPLAELTEEEKYEQELRKTQLIKAAPAAKTSSVFED
          L..G.R..PG....RWSR.GPE.K.PRID.EYYRKP...................IKAAPAAKTSS..ED
Retrocopy LSCGFRASPG----RWSRRGPESKGPRIDREYYRKPXXXXXXXXXXXXXXXXXXXIKAAPAAKTSSGCED

Parental  PVISKFTNMMMKGGNKVLARSLMMQTLEAVK-RKQFEKYHAASAEEQATIERNPYVIFHQA-LQNCEPVI
          PVISKFT.MMMKGGN.VLARSL..QT....K.........A...E..A..ERN.....H.A.LQ.CEPVI
Retrocopy PVISKFTDMMMKGGNGVLARSLLVQTRSCEK>KQFEKYHAASAEEQ-ASRERNRRAVSHPA<LQSCEPVI

Parental  GLVPILRGGHFYQVPVPLADRRRRFLAMKWMIKECREKKHRRMLMPEKLSHELLEAFHNQGPVIKKKHDM
          GLVPILRGG.FYQ.PVPLA.RRRRFLAMKWMIKECREKKHRRMLMPEKLSHE.LEAFHNQGPVIKKK.DM
Retrocopy GLVPILRGGRFYQGPVPLARRRRRFLAMKWMIKECREKKHRRMLMPEKLSHEPLEAFHNQGPVIKKKRDM

Parental  HKMAEANRALAHYRWW
          HK.AEA.RA.A..R.W
Retrocopy HKTAEASRARARCRRW

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	0.04 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_438 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_438 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,