RetrogeneDB ID: retro_cfam_77

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:40377078..40377873(-)
• Located in intron of: ENSCAFG00000019696

Retrocopy information

• Ensembl ID: ENSCAFG00000024468
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS3A
• Ensembl ID: ENSCAFG00000007990
• Aliases: None
• Description: 40S ribosomal protein S3a [Source:UniProtKB/TrEMBL;Acc:F2Z4Q5]

Sequence

>retro_cfam_77
ATGGCGGTCAGCAAGAACAAGCGCCTTACAAAAGGCGGCAAAAAGGGAACCAAGAAGAAAGTGGTTGATCCATTTTCTAA
GAAAGATTGGTATGATGTGAAAGCACCAGCTATGTTCAATATAAGAAATATTGGAAAAACACTAGTCACAAGAACTCAAG
GAACCAAAATTGCGTCTGATGGTCTCAAGGGTCGCGTTTTTGAAGTTAGCCTTGCTGATCTGCAGAATGATGAAGTTGCA
TTTAGGAAATTCAAGCTAATCACTGAGGATGTGCAGGGTAAAAACTGCCTGACTAATTTCCATGGCATGGATCTTACCCG
TGACAAAATGTGCTCCATGGTCAAAAAATGGCAGACCATGATTGAAGCTCATGTTGATGTAAAGACTACCGATGGTTATT
TGCTTCGTCTATTTTGTGTTGGTTTTACTAAAAAACGCAATAATCAGATTCGGAAGACCTCTTACGCTCAGCACCAACAG
GTCTGCCAAAACCGGAAAAAGATGATGGAAATCATGACCCAAGAGGTGCAGACAAATGACTTGAAAGAAGTGGTCAATAA
ATTGATTCCAGACAGCATCGGAAAAGATATAGAAAAAGCTTGTCAGTCTATTTATCCACTCCATGATGTTTTTGTTAGAA
AAGTAAAAATGCTGACAAAGCCCAAGTTTGAATCGGGAAAACTCATGGAGCTTTATGGTGAAGGTAGTAGTTCTGGAAAA
GCTATGGGGGATGAGACCGGTGCTAAAGTTGAACGAGCTGATGGATATGAACCACCAGTCCAAGAATCTGTTTAA

Alignment

ORF - retro_cfam_77 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
          MAV.KNKRLTKGGKKG.KKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
Retrocopy MAVSKNKRLTKGGKKGTKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS

Parental  LADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
          LADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
Retrocopy LADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV

Parental  GFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDV
          GFTKKRNNQIRKTSYAQHQQV.Q.RKKMMEIMT.EVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDV
Retrocopy GFTKKRNNQIRKTSYAQHQQVCQNRKKMMEIMTQEVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDV

Parental  FVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVERADGYEPPVQESV
          FVRKVKML.KPKFE.GKLMEL.GEGSSSGKA.GDETGAKVERADGYEPPVQESV
Retrocopy FVRKVKMLTKPKFESGKLMELYGEGSSSGKAMGDETGAKVERADGYEPPVQESV

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	249.60 RPM
SRP017611_brain	0.16 RPM	81.06 RPM
SRP017611_kidney	0.00 RPM	772.37 RPM
SRP017611_liver	0.36 RPM	161.41 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_77 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_77 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_77 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018425	11 retrocopies	retro_amel_1333, retro_amel_1361, retro_amel_1380, retro_amel_1514, retro_amel_159, retro_amel_1697, retro_amel_1732, retro_amel_1739, retro_amel_230, retro_amel_367, retro_amel_863,
Bos taurus	ENSBTAG00000009908	3 retrocopies	retro_btau_1284, retro_btau_1733, retro_btau_233,
Canis familiaris	ENSCAFG00000007990	7 retrocopies	retro_cfam_103, retro_cfam_146, retro_cfam_169, retro_cfam_170, retro_cfam_179, retro_cfam_222, retro_cfam_77 ,
Callithrix jacchus	ENSCJAG00000002268	7 retrocopies	retro_cjac_2, retro_cjac_21, retro_cjac_249, retro_cjac_312, retro_cjac_337, retro_cjac_368, retro_cjac_78,
Dipodomys ordii	ENSDORG00000002250	10 retrocopies	retro_dord_142, retro_dord_168, retro_dord_193, retro_dord_209, retro_dord_229, retro_dord_314, retro_dord_380, retro_dord_752, retro_dord_757, retro_dord_95,
Erinaceus europaeus	ENSEEUG00000004994	4 retrocopies	retro_eeur_297, retro_eeur_510, retro_eeur_517, retro_eeur_66,
Gorilla gorilla	ENSGGOG00000003182	2 retrocopies	retro_ggor_70, retro_ggor_97,
Microcebus murinus	ENSMICG00000004921	9 retrocopies	retro_mmur_1230, retro_mmur_1289, retro_mmur_193, retro_mmur_299, retro_mmur_330, retro_mmur_526, retro_mmur_592, retro_mmur_626, retro_mmur_945,
Macaca mulatta	ENSMMUG00000021821	1 retrocopy	retro_mmul_2297,
Monodelphis domestica	ENSMODG00000000969	6 retrocopies	retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mus musculus	ENSMUSG00000028081	2 retrocopies	retro_mmus_218, retro_mmus_254,
Oryctolagus cuniculus	ENSOCUG00000007011	1 retrocopy	retro_ocun_257,
Rattus norvegicus	ENSRNOG00000011893	1 retrocopy	retro_rnor_198,
Sarcophilus harrisii	ENSSHAG00000015088	2 retrocopies	retro_shar_777, retro_shar_95,
Vicugna pacos	ENSVPAG00000004235	8 retrocopies	retro_vpac_253, retro_vpac_31, retro_vpac_322, retro_vpac_439, retro_vpac_486, retro_vpac_497, retro_vpac_529, retro_vpac_88,