RetrogeneDB ID: retro_cfam_671

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:195855..196128(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000005339
• Aliases: None
• Description: None

Sequence

>retro_cfam_671
GTTCACACAATCACCAGAAAGCCCATGTCTTGGCACGAGAACCTGGAGGAACCTGCAGATGCCGAGTTCCTAAATCTTAT
CCACCATGTCACTCAGGGGTCATGGAAGAAATACCCAGACACGCAAACAGAAATCCAAGAAATTGGATGGGACTCTGAGC
CCTAGGTCAGCCCGGAACGTGATGAACGCAGGCTGAACCATGTCAGGGTGCACAGCGATATCACGCTCCACAAGGCTAAA
GTGTGGAGCTTGCGAGAAGATGATTGCCACACA

Alignment

ORF - retro_cfam_671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.81 %
• Parental protein coverage: 62.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHTITRKPMSWHENLEEPADARFLNLIHHAAQGPRKKYPDTQTESQEIGWDSEPLVSPERDDRRLNHFRV
          VHTITRKPMSWHENLEEPADA.FLNLIHH..QG..KKYPDTQTE.QEIGWDSEP.VSPERD.RRLNH.RV
Retrocopy VHTITRKPMSWHENLEEPADAEFLNLIHHVTQGSWKKYPDTQTEIQEIGWDSEP*VSPERDERRLNHVRV

Parental  HSDITLYKAKVWSLGEDDRHT
          HSDITL.KAKVWSL.EDD.HT
Retrocopy HSDITLHKAKVWSLREDDCHT

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	0.80 RPM
SRP017611_brain	0.00 RPM	0.16 RPM
SRP017611_kidney	0.00 RPM	0.07 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_671 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_671 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005339	1 retrocopy	retro_cfam_671 ,
Callithrix jacchus	ENSCJAG00000003315	1 retrocopy	retro_cjac_323,
Homo sapiens	ENSG00000186973	1 retrocopy	retro_hsap_1,
Gorilla gorilla	ENSGGOG00000010892	2 retrocopies	retro_ggor_1704, retro_ggor_69,
Nomascus leucogenys	ENSNLEG00000013230	3 retrocopies	retro_nleu_147, retro_nleu_2537, retro_nleu_2865,
Pongo abelii	ENSPPYG00000001457	1 retrocopy	retro_pabe_48,
Pan troglodytes	ENSPTRG00000000624	1 retrocopy	retro_ptro_22,