RetrogeneDB ID: retro_cfam_180

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:2985544..2986030(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000030774
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000032245
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:J9NZK4]

Sequence

>retro_cfam_180
ATGTCAGTGACACTGCATACAGATGTAGGTGATATTAAAATTGAAGTATTCTGTGAGAGGACACCCAAAACTTGTGAGAA
TTTCTTGGCTCTTTGTGCCAGTAATTACTACAATGGCTGTATATTTCATAGAAATATCAAGGGTTTCATGGTTCAAACAG
GAGATCCGACAGGTACCGGAAGAGGAGGTAACAGTATCTGGGGCAAGAAATTTGAGGATGAATATAGTGAATATCTTAAG
CACAATGTTAGGGGTGTTGTATCAATGGCTAATAATGGCCCAAACACCAATGGATCTCAGTTCTTCATCACCTATGGCAA
ACAGCCACATTTGGACATGAAATACACGGTATTTGGAAAGGTAATAGATGGTCTAGAAACTCTAGATGAATTGGAGAAGT
TACCAGTAAATGAGAAGACCTACTGGCCTCTTAATGACGTACACATTAAGGACAAAACTATTCATGCCAATCCATTTGCA
CAATAG

Alignment

ORF - retro_cfam_180 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTGRGGNSIWGKKF
          SVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTGRGGNSIWGKKF
Retrocopy SVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTGRGGNSIWGKKF

Parental  EDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGKVIDGLETLDELEKLPVNEKTY
          EDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGKVIDGLETLDELEKLPVNEKTY
Retrocopy EDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGKVIDGLETLDELEKLPVNEKTY

Parental  RPLNDVHIKDITIHANPFAQ
          .PLNDVHIKD.TIHANPFAQ
Retrocopy WPLNDVHIKDKTIHANPFAQ

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	1.22 RPM	5.59 RPM
SRP017611_brain	0.48 RPM	4.13 RPM
SRP017611_kidney	1.25 RPM	4.29 RPM
SRP017611_liver	0.58 RPM	1.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_180 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_180 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005917	1 retrocopy	retro_amel_1458,
Bos taurus	ENSBTAG00000005416	1 retrocopy	retro_btau_1585,
Canis familiaris	ENSCAFG00000017053	1 retrocopy	retro_cfam_1999,
Canis familiaris	ENSCAFG00000032245	1 retrocopy	retro_cfam_180 ,
Dasypus novemcinctus	ENSDNOG00000002364	1 retrocopy	retro_dnov_2477,
Dipodomys ordii	ENSDORG00000007389	1 retrocopy	retro_dord_575,
Monodelphis domestica	ENSMODG00000015037	1 retrocopy	retro_mdom_1025,
Tupaia belangeri	ENSTBEG00000000664	1 retrocopy	retro_tbel_4520,