RetrogeneDB ID: retro_cfam_1063

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:4663137..4663376(-)
• Located in intron of: ENSCAFG00000004478

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAPC5
• Ensembl ID: ENSCAFG00000017304
• Aliases: None
• Description: small nuclear RNA activating complex, polypeptide 5, 19kDa [Source:HGNC Symbol;Acc:15484]

Sequence

>retro_cfam_1063
ACGCTGCTCCGGCTGAAGGTGGCCCTGACGACCAGCTGAATCGGCTCAAGGTTGAAGAACTAGCCCTCCAGTCAATGATT
AGTTCGAGGAGAGGAGATGAGATGCTTTATTCTCACCTTGCACCTCAACAGTCACATGATATGCTGGTGCATGTGGACAA
TGAAGCATCAGTCACAACCAAACTGCACTGGAGTTGAGCACAAGATGTGCCCGAAGAGTAGTAGGAGGAAGAAGCAGAT

Alignment

ORF - retro_cfam_1063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.08 %
• Parental protein coverage: 82. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLLRLKAAL-HDQLNRLKVEELALQSMISSRRGDETLSSQPAPEQSHDQMLVHVDNEASINQTALELSTR
          TLLRLK.AL..DQLNRLKVEELALQSMISSRRGDE.L.S..AP.QSHD.MLVHVDNEAS...T.L..S..
Retrocopy TLLRLKVAL<DDQLNRLKVEELALQSMISSRRGDEMLYSHLAPQQSHD-MLVHVDNEASVT-TKLHWS*A

Parental  SHVLEEEEEEEEE
          ..V.EE..EEE..
Retrocopy QDVPEE**EEEAD

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	5.25 RPM
SRP017611_brain	0.08 RPM	3.26 RPM
SRP017611_kidney	0.00 RPM	3.50 RPM
SRP017611_liver	0.22 RPM	1.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1063 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1063 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1063 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017304	1 retrocopy	retro_cfam_1063 ,
Callithrix jacchus	ENSCJAG00000007484	1 retrocopy	retro_cjac_2314,
Dasypus novemcinctus	ENSDNOG00000006689	1 retrocopy	retro_dnov_1203,
Gorilla gorilla	ENSGGOG00000003693	1 retrocopy	retro_ggor_2398,
Macropus eugenii	ENSMEUG00000003990	1 retrocopy	retro_meug_1590,
Macaca mulatta	ENSMMUG00000016841	1 retrocopy	retro_mmul_1815,
Mus musculus	ENSMUSG00000032398	1 retrocopy	retro_mmus_702,
Nomascus leucogenys	ENSNLEG00000012935	1 retrocopy	retro_nleu_2325,
Oryctolagus cuniculus	ENSOCUG00000008791	1 retrocopy	retro_ocun_1059,
Rattus norvegicus	ENSRNOG00000010156	1 retrocopy	retro_rnor_1087,
Ictidomys tridecemlineatus	ENSSTOG00000009201	1 retrocopy	retro_itri_1582,
Tupaia belangeri	ENSTBEG00000014333	1 retrocopy	retro_tbel_68,