RetrogeneDB ID: retro_cfam_760

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:35732820..35733291(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000007091
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRAPPC4
• Ensembl ID: ENSCAFG00000012383
• Aliases: None
• Description: trafficking protein particle complex 4 [Source:HGNC Symbol;Acc:19943]

Sequence

>retro_cfam_760
GTGCTGGCCATCAATGGCGTGGACGTGAACGGCAAGTTCACGGCTGATGGGAAAGAGGTGCTGGGGTACTTGAGCAATCC
TGCCAATTACCCGGTGTCTATTCGATCTGGCCGACCTCGCCTCACCTCCAATGAGAAGCTTATGTTGGCCTCTATGTTCC
ACTCGCTGTTTGCAATCGGTTCCCAGCTGTCTCCAGAACAGGGCAGCTCAGGCACTGAGATGCTGGAGACCGACTCGTGC
AAACTGCACTGCTTCCAGACACTGACAGGGATCAAGTTTGCGGTGCTGGCGAATCCTAGGCAAGCGGGAATAGATTCTCT
TCTCCAAAAGATTTATGAGATCTACTCAGACTTTGCCCTCAAGAATCCATTCTACTCCCTCGAAATGCCCATCAGGTGTG
AGCTGTTTGACCAGAACCTGGAGTTAGCCCTGGAGGTGGCAGAGAAGGCTGGAACTTTTGGGCCTGGATCA

Alignment

ORF - retro_cfam_760 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.99 %
• Parental protein coverage: 71.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLAINGVDVNGKYTADGKEVLEYLGNPANYPVSIRFGRPRLTSNEKLMLASMFHSLFAIGSQLSPEQGSS
          VLAINGVDVNGK.TADGKEVL.YL.NPANYPVSIR.GRPRLTSNEKLMLASMFHSLFAIGSQLSPEQGSS
Retrocopy VLAINGVDVNGKFTADGKEVLGYLSNPANYPVSIRSGRPRLTSNEKLMLASMFHSLFAIGSQLSPEQGSS

Parental  GIEMLETDTFKLHCFQTLTGIKFVVLADPRQAGIDSLLRKIYEIYSDFALKNPFYSLEMPIRCELFDQNL
          G.EMLETD..KLHCFQTLTGIKF.VLA.PRQAGIDSLL.KIYEIYSDFALKNPFYSLEMPIRCELFDQNL
Retrocopy GTEMLETDSCKLHCFQTLTGIKFAVLANPRQAGIDSLLQKIYEIYSDFALKNPFYSLEMPIRCELFDQNL

Parental  KLALEVAEKAGTFGPGS
          .LALEVAEKAGTFGPGS
Retrocopy ELALEVAEKAGTFGPGS

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	19.28 RPM
SRP017611_brain	0.00 RPM	12.78 RPM
SRP017611_kidney	0.07 RPM	29.52 RPM
SRP017611_liver	0.00 RPM	13.12 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_760 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_760 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_760 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012383	1 retrocopy	retro_cfam_760 ,
Callithrix jacchus	ENSCJAG00000013703	1 retrocopy	retro_cjac_450,
Dasypus novemcinctus	ENSDNOG00000007885	1 retrocopy	retro_dnov_46,
Myotis lucifugus	ENSMLUG00000004759	1 retrocopy	retro_mluc_1438,
Ictidomys tridecemlineatus	ENSSTOG00000014340	1 retrocopy	retro_itri_1252,