RetrogeneDB ID: retro_cfam_1359

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:87042722..87043242(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A14
• Ensembl ID: ENSCAFG00000018766
• Aliases: SLC25A14, BMCP-1, Ucp5
• Description: None

Sequence

>retro_cfam_1359
CCACCATTGCCTAGGCAATGACCTGGCTACTTCCTTGGTCTCAGTGCCTCCATTTTGGGGTTGCCATAGCATTTCAGACA
GTGGGAGCTGGGGCTTCCCGTAATCCTGAGCACCAAGAAAGAGCCACTGCAAGCCCTGAGATGTCTGGTCTGAATTGGAA
ACCCTTTGTATATAGCAGCCTTGCCTCTATTGTTGCTGAATTTGGAGTTGCCCTGTGGGCCAAAATGCAATTTCAAGTTC
AAGACCAAAGCACCGATGTCCACTTTAAAAGGATCAAATACTGAGGAATGTTTCATACCTTGCTCCAAATCTATAAAGAA
GGTATATGGGCTCTGTATTCTGTAATTCTCCTGCTTTCCTAAGAAAGGCATCATATGGCTCCATTAAAATTCACATTTAC
TAAAGCTTAAAGATAGTATTTGTAGAATATTTAGAAGATGGAACTCTTCTAATTAATATGATCCTGAGTTGTGTCAGGAG
TGATATCTTCCACTATAGCCAATCCACTGATATAATAAAG

Alignment

ORF - retro_cfam_1359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.61 %
• Parental protein coverage: 52.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPLLRRRLGYFR-WSQCFRVGIAVAFPTVGASASQSSAEPEQHQNSATVSHEMSGLNWKPFVYGGLASIV
          PPL.R...GYF..WSQC...G.A.AF.TVGA.AS........HQ..AT.S.EMSGLNWKPFVY..LASIV
Retrocopy PPLPRQ*PGYFL<WSQCLHFGVAIAFQTVGAGASRNP----EHQERATASPEMSGLNWKPFVYSSLASIV

Parental  AEFGTFPVDLTKTRLQVQGQSIDVRFKEIKYRGMFHALFRIYKEEGVLALYSGI-APALLRQASYGTIKI
          AEFG...........Q.Q..S.DV.FK.IKY.GMFH.L..IYK.EG..ALYS.I..PA.LR.ASYG.IKI
Retrocopy AEFGVALWAKMQFQVQDQ--STDVHFKRIKY*GMFHTLLQIYK-EGIWALYSVI<SPAFLRKASYGSIKI

Parental  GIYQSLKRLFVERLEDETLLINMICGVVSGVISSTIANPTDVLK
          .IY.SLK..FVE.LED.TLLINMI...V...I.......TD..K
Retrocopy HIY*SLKIVFVEYLEDGTLLINMILSCVRSDIFH-YSQSTDIIK

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	11.59 RPM
SRP017611_brain	0.00 RPM	12.31 RPM
SRP017611_kidney	0.00 RPM	6.41 RPM
SRP017611_liver	0.07 RPM	0.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1359 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1359 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016263	1 retrocopy	retro_btau_1362,
Canis familiaris	ENSCAFG00000018766	1 retrocopy	retro_cfam_1359 ,
Callithrix jacchus	ENSCJAG00000002456	1 retrocopy	retro_cjac_2257,
Homo sapiens	ENSG00000102078	1 retrocopy	retro_hsap_2954,
Macaca mulatta	ENSMMUG00000008386	1 retrocopy	retro_mmul_1943,
Nomascus leucogenys	ENSNLEG00000015318	1 retrocopy	retro_nleu_1638,
Pongo abelii	ENSPPYG00000020715	2 retrocopies	retro_pabe_2450, retro_pabe_3595,
Pan troglodytes	ENSPTRG00000022268	1 retrocopy	retro_ptro_2048,
Tursiops truncatus	ENSTTRG00000016206	2 retrocopies	retro_ttru_1159, retro_ttru_1570,