RetrogeneDB ID: retro_cfam_436

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:68119338..68119728(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPS23
• Ensembl ID: ENSCAFG00000030896
• Aliases: None
• Description: ribosomal protein S23 [Source:HGNC Symbol;Acc:10410]

Sequence

>retro_cfam_436
ATGGACAAGTGTCAAGGTATTTGTACTGGCAGGAAGCTCTGTGGCCACTGACAAGAGCAGACGTGGCATGATAAACAGAA
CAAGAAAGCTTATTTGGATACAGCCCGAAGGCCAGCCCTTTCGGAGGCACTTCCCATACAAAGGGAATTGTGCTGGGAAA
AGTAGGGTAGAAGCCAAACAGACAAATTCTGCCATCAGGAAGTGTGTCAGGGTCCAGCTGATCAAAAGTGGAGGAAAAAA
TCACAGCCTTTGTACCCAATGATGGTTGTCTGAATTTTAGTGAGGAAAATGATGGAAGTTCTGATTGCTGGATTTGATTG
CAAAGGTCATGCTGTCGGTAACATTCCTGTTGTTCATTTTAAGGTTGTTGAAATAGCCAATGTCTCTCTT

Alignment

ORF - retro_cfam_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.88 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTAL-KANPFGGASHAKGIVLEKVG-VEAKQPNSAIRK
          M.KC.G..T.RKL..H...Q.WHDKQ.KKA.L.TA..KA.PFGG.SH.KGIVL.KVG.VEAKQ.NSAIRK
Retrocopy MDKCQGICTGRKLCGH*QEQTWHDKQNKKAYLDTAR<KASPFGGTSHTKGIVLGKVG<VEAKQTNSAIRK

Parental  CVRVQLIKNG-KKITAFVPNDGCLNFIEEND-EVLVAGFGRKGHAVGDIPGVRFKVVKVANVSL
          CVRVQLIK.G..KITAFVPNDGCLNF.EEND.EVL.AGF..KGHAVG.IP.V.FKVV..ANVSL
Retrocopy CVRVQLIKSG>EKITAFVPNDGCLNFSEEND>EVLIAGFDCKGHAVGNIPVVHFKVVEIANVSL

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	263.92 RPM
SRP017611_brain	0.00 RPM	66.29 RPM
SRP017611_kidney	0.00 RPM	327.48 RPM
SRP017611_liver	0.00 RPM	154.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_436 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_436 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_436 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013358	3 retrocopies	retro_btau_173, retro_btau_205, retro_btau_80,
Canis familiaris	ENSCAFG00000030896	7 retrocopies	retro_cfam_1145, retro_cfam_1305, retro_cfam_1415, retro_cfam_1743, retro_cfam_2105, retro_cfam_375, retro_cfam_436 ,
Callithrix jacchus	ENSCJAG00000011247	2 retrocopies	retro_cjac_126, retro_cjac_256,
Dipodomys ordii	ENSDORG00000001813	2 retrocopies	retro_dord_187, retro_dord_93,
Macropus eugenii	ENSMEUG00000012931	1 retrocopy	retro_meug_811,
Macaca mulatta	ENSMMUG00000003578	4 retrocopies	retro_mmul_1239, retro_mmul_1974, retro_mmul_2305, retro_mmul_852,
Pteropus vampyrus	ENSPVAG00000002083	4 retrocopies	retro_pvam_1483, retro_pvam_782, retro_pvam_80, retro_pvam_922,
Sarcophilus harrisii	ENSSHAG00000008347	2 retrocopies	retro_shar_257, retro_shar_348,
Vicugna pacos	ENSVPAG00000009427	7 retrocopies	retro_vpac_195, retro_vpac_239, retro_vpac_393, retro_vpac_543, retro_vpac_56, retro_vpac_598, retro_vpac_81,