RetrogeneDB ID: retro_cfam_635

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:36097992..36098286(-)
• Located in intron of: ENSCAFG00000002731

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM254
• Ensembl ID: ENSCAFG00000015748
• Aliases: None
• Description: transmembrane protein 254 [Source:HGNC Symbol;Acc:25804]

Sequence

>retro_cfam_635
CTAGGACTTAACCGTTGGGGTTGTCTTCTGGCCTCAGAGTATCCCTTATCAGAGCCTTGGGCCTCTGGGCCTTTTCACTC
AGGACTTGGACTGTCATCACACCCTCCTGCACAATGGGTGTTGGTTTGCCTGGCTGATTGACATGGGAGAGTCTTTGTAA
CCATGGTTTTGAGCAAATATAAAGGCATCACAAATGGCCGGGCTCAACTATTCTGGTTCCTATAAACTTTCCTCTTTGGG
ATAGCGTCTCTCTCCATCTTGATTGCTTATAGACCAAAATGCCAAAAGCACACT

Alignment

ORF - retro_cfam_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.25 %
• Parental protein coverage: 66.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGYMAW-VVFWPQSVPYQSLGPLGLFTQYLVDHHHTLLHSGYWLAWLIHVGESL-YAILLVRSKGITNGR
          LG...W.VVFWPQS.PYQSLGPLGLFTQ.L.D.HHTLLH.G.W.AWLI..GESL.....L...KGITNGR
Retrocopy LGLNRW>VVFWPQSIPYQSLGPLGLFTQDL-DCHHTLLHNGCWFAWLIDMGESL<VTMVLSKYKGITNGR

Parental  AQLLWFLQTFLFGIASLSILIAYRPKRQKQT
          AQL.WFL.TFLFGIASLSILIAYRPK.QK.T
Retrocopy AQLFWFL*TFLFGIASLSILIAYRPKCQKHT

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	24.11 RPM
SRP017611_brain	0.00 RPM	12.46 RPM
SRP017611_kidney	0.00 RPM	21.92 RPM
SRP017611_liver	0.00 RPM	3.19 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_635 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_635 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_635 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015748	3 retrocopies	retro_cfam_602, retro_cfam_635 , retro_cfam_637,
Callithrix jacchus	ENSCJAG00000007670	1 retrocopy	retro_cjac_3839,
Dasypus novemcinctus	ENSDNOG00000024625	1 retrocopy	retro_dnov_555,
Felis catus	ENSFCAG00000026147	1 retrocopy	retro_fcat_401,
Myotis lucifugus	ENSMLUG00000007585	16 retrocopies	retro_mluc_1178, retro_mluc_2482, retro_mluc_2491, retro_mluc_2492, retro_mluc_2528, retro_mluc_2532, retro_mluc_2550, retro_mluc_2551, retro_mluc_2552, retro_mluc_2572, retro_mluc_2573, retro_mluc_2583, retro_mluc_2586, retro_mluc_2603, retro_mluc_2623, retro_mluc_766,
Macaca mulatta	ENSMMUG00000003015	1 retrocopy	retro_mmul_1583,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Tarsius syrichta	ENSTSYG00000006920	1 retrocopy	retro_tsyr_103,
Tursiops truncatus	ENSTTRG00000006122	1 retrocopy	retro_ttru_454,