RetrogeneDB ID: retro_cfam_551

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:39485018..39485266(+)
• Located in intron of: ENSCAFG00000001816

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D1
• Ensembl ID: ENSCAFG00000000811
• Aliases: None
• Description: None

Sequence

>retro_cfam_551
GTGGCATTTTCTGTTCTATTAGCTGGATTACTGTGGCTTTCTGGTGGCATAAGACTTTTTCACAGTGTTCCATACCCTTG
GAAATACTGGCTGCATTAGCCAGTATATGCTTTTTAATGGGACTCATGAAAAAAATGTGGGAAACAGTTGTTTATAATAA
TTCTTATGTTTTTGTGATTAATGTTTACAGTCTGGTTGCTTCTCTTTGGTCGTATGGGAGGAGACTGGCCTTATTATTCT
GCAATTTG

Alignment

ORF - retro_cfam_551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.27 %
• Parental protein coverage: 54.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IFFSILGTGLLWLPGGIKLF-AVFYTLGN-LSALASTCFLMGPMKQLKKMFETTRLLATIIMLLCLIFTL
          ..FS.L..GLLWL.GGI.LF..VF.TLGN.L.ALAS.CFLMG.MK...KM.ET................L
Retrocopy VAFSVLLAGLLWLSGGIRLF>TVFHTLGN>LAALASICFLMGLMK---KMWETVVYNNSYVFVI-NVYSL

Parental  CAALWWHKKGLALLFCIL
          .A.LW.....LALLFC.L
Retrocopy VASLWSYGRRLALLFCNL

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	19.32 RPM
SRP017611_brain	0.00 RPM	18.50 RPM
SRP017611_kidney	0.00 RPM	52.30 RPM
SRP017611_liver	0.00 RPM	20.09 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_551 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_551 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009311	3 retrocopies	retro_amel_1244, retro_amel_1452, retro_amel_374,
Bos taurus	ENSBTAG00000002993	5 retrocopies	retro_btau_1458, retro_btau_1460, retro_btau_31, retro_btau_546, retro_btau_900,
Canis familiaris	ENSCAFG00000000811	2 retrocopies	retro_cfam_283, retro_cfam_551 ,
Equus caballus	ENSECAG00000019479	1 retrocopy	retro_ecab_1029,
Mus musculus	ENSMUSG00000073468	1 retrocopy	retro_mmus_164,
Oryctolagus cuniculus	ENSOCUG00000001200	1 retrocopy	retro_ocun_1492,
Otolemur garnettii	ENSOGAG00000006302	1 retrocopy	retro_ogar_1601,
Ochotona princeps	ENSOPRG00000003408	2 retrocopies	retro_opri_37, retro_opri_809,
Pongo abelii	ENSPPYG00000017165	1 retrocopy	retro_pabe_181,
Pteropus vampyrus	ENSPVAG00000012673	3 retrocopies	retro_pvam_1340, retro_pvam_465, retro_pvam_559,
Sus scrofa	ENSSSCG00000004020	1 retrocopy	retro_sscr_751,
Tupaia belangeri	ENSTBEG00000000045	2 retrocopies	retro_tbel_3277, retro_tbel_747,
Tursiops truncatus	ENSTTRG00000004447	2 retrocopies	retro_ttru_1353, retro_ttru_624,