RetrogeneDB ID: retro_cfam_229

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:37301743..37302190(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000024419
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000023207
• Aliases: None
• Description: None

Sequence

>retro_cfam_229
GTGACCAACGAGGAACCTCTTCCAAAAAAGGTTCGACTGAGTGAAACAGACATCAAAGTTATGGCACGAGAGGAGTTCAT
TCTAAGGTGGAAACAATATGAAGCATATGTCCAAGCTTTGGAGGGCAAGTACACAGATCTTAATTCTAATGATGGGTTAA
GGGAGTCTGAAGAAAAACTAAAGCAACAACAAGAGTCTGCTCGCAGGGAAAGCATCCTTGTAATGCGACTAGAAACCAAG
GAGCAAGAGGTGCAAGAGTGTACTACTCAAATCCAGTACTTTAAGCAAGTCCAGCAGCCTAACGTTGCCCAACTGAGATC
AACAATGGTAGACCCAGCGATCAACTTGTTTTTCCTCAAAATGAAAGGTGAACTAGAACAGACTAAAGACAACCTGGAAC
AAGCCCAAAATGAACTGAGTGCCTGGAAGTTTATGCCTGATAGGTAA

Alignment

ORF - retro_cfam_229 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.67 %
• Parental protein coverage: 55.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTNEEPLPKKVRLSETDFKVMARDELILRWKQYEAYVQALEGKYTDLNSNDVTGLRESEEKLKQQQQESA
          .TNEEPLPKKVRLSETD.KVMAR.E.ILRWKQYEAYVQALEGKYTDLNSND..GLRESEEKLKQQQ.ESA
Retrocopy VTNEEPLPKKVRLSETDIKVMAREEFILRWKQYEAYVQALEGKYTDLNSND--GLRESEEKLKQQQ-ESA

Parental  RRENILVMRLATKEQEMQECTTQIQYLKQVQQPSVAQLRSTMVDPAINLFFLKMKGELEQTKDKLEQAQN
          RRE.ILVMRL.TKEQE.QECTTQIQY.KQVQQP.VAQLRSTMVDPAINLFFLKMKGELEQTKD.LEQAQN
Retrocopy RRESILVMRLETKEQEVQECTTQIQYFKQVQQPNVAQLRSTMVDPAINLFFLKMKGELEQTKDNLEQAQN

Parental  ELSAWKFTPD
          ELSAWKF.PD
Retrocopy ELSAWKFMPD

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	57.58 RPM
SRP017611_brain	0.00 RPM	29.93 RPM
SRP017611_kidney	0.00 RPM	47.55 RPM
SRP017611_liver	0.00 RPM	21.68 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_229 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_229 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007974	1 retrocopy	retro_btau_486,
Canis familiaris	ENSCAFG00000023207	2 retrocopies	retro_cfam_188, retro_cfam_229 ,
Myotis lucifugus	ENSMLUG00000000721	1 retrocopy	retro_mluc_1297,