RetrogeneDB ID: retro_cfam_2156

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:44387746..44388044(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000015965
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SMIM14
• Ensembl ID: ENSCAFG00000023287
• Aliases: None
• Description: small integral membrane protein 14 [Source:HGNC Symbol;Acc:27321]

Sequence

>retro_cfam_2156
ATGGCAGAAGGTGGATTCGATCCTCGTGAATGTGTTTGCTCTCATGAGCAGCATGCAATGAGAAGGCTGATCAATTTCTT
GAGGCAGTCTCAGTCCTACTGCACAGACAGCATGTCTTCAGGAATTACCAGGGCCCTCTGGTGATAATGGCATCAGTATT
ACCATGATCTTGATGACCTGGATGGTTATTGCAGTGATCTTGTTTCTACTGAGACCTCCTAATTTAAGAGGATCCAACCT
AACTGGCAAGCCAACCAGTCCTCATAATGGACAAGATCCAACAGCCCCTCCTGTGGAC

Alignment

ORF - retro_cfam_2156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEGGFDPCECVCSHE-HAMRRLINLLRQSQSYCTDT-ECLQELPGP-SGDNGISITMILMAWMVIAVIL
          MAEGGFDP.ECVCSHE.HAMRRLIN.LRQSQSYCTD.........GP.SGDNGISITMILM.WMVIAVIL
Retrocopy MAEGGFDPRECVCSHEQHAMRRLINFLRQSQSYCTDS<HVFRNYQGP<SGDNGISITMILMTWMVIAVIL

Parental  FLLRPPNLRGSNLTGKPTSPHNGQDPPAPPVD
          FLLRPPNLRGSNLTGKPTSPHNGQDP.APPVD
Retrocopy FLLRPPNLRGSNLTGKPTSPHNGQDPTAPPVD

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	13.10 RPM
SRP017611_brain	0.08 RPM	13.34 RPM
SRP017611_kidney	0.00 RPM	45.83 RPM
SRP017611_liver	0.00 RPM	37.78 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2156 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2156 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023287	1 retrocopy	retro_cfam_2156 ,
Dipodomys ordii	ENSDORG00000001693	2 retrocopies	retro_dord_468, retro_dord_570,
Homo sapiens	ENSG00000163683	1 retrocopy	retro_hsap_3836,
Loxodonta africana	ENSLAFG00000002601	2 retrocopies	retro_lafr_1038, retro_lafr_158,
Mustela putorius furo	ENSMPUG00000006076	1 retrocopy	retro_mputfur_641,
Nomascus leucogenys	ENSNLEG00000017113	1 retrocopy	retro_nleu_2132,
Otolemur garnettii	ENSOGAG00000007152	4 retrocopies	retro_ogar_1971, retro_ogar_3123, retro_ogar_3370, retro_ogar_740,