RetrogeneDB ID: retro_cfam_602

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:37337981..37338432(+)
• Located in intron of: ENSCAFG00000002784

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_602
GGTGGGGACAGAGACAGCTCCCCATCCCAAGACTCAGTATGTAGATCTTTCAAGATGGTGGTGATGAAGTCTGAGGCCGG
CAGGGCTGCTTCCACTTACTTCCGTCCAGCCAAATATTTGCTGGTCATTGTCACTGGTCATTGTCCTGGCACTGGGCTAT
TTTGTGGGTTGTCTTCTGACCACAGAGTATTATCCCTTATCAGAGCTTTGGGCCTCTGGGACTCTTCACTCAGGACTTGG
TGTACCATCATCATCACACCCTCCTGCACAATGGGTGTTGGCTTGTCTGGCTGATCAACATGGGAGAGTCCTTGTAGCCA
TGGTTTTGTGCAAGTGAAAAGGCATAACGAATACTAGGCCTCAACTACTCTGGTTCCTACAAATCTTCCTCTTTGGGATA
GGGTCTCTTTCCATCTTGATTGCTTACAGACCAAAATGCCAAAAACACACG

Alignment

ORF - retro_cfam_602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.17 %
• Parental protein coverage: 98.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGAAGMAPAAGGEAHFQRMVPLKSEAGRAASAYFRPARRLPALVT-VLAL--GYMAWVVFWPQSVPYQSL
          GG.....P..........MV..KSEAGRAAS.YFRPA..L...VT.V..L..GY...........P...L
Retrocopy GGDRDSSPSQDSVCRSFKMVVMKSEAGRAASTYFRPAKYLLVIVT>VIVLALGYFVGCLLTTEYYPLSEL

Parental  -GPLGLFTQYLV-DHHHTLLHSGYWLAWLIHVGES-LYAILLVRSKGITNGRAQLLWFLQTFLFGIASLS
          .GPLGLFTQ.LV..HHHTLLH.G.WL.WLI..GES.L.A..L...KGITN.R.QLLWFLQ.FLFGI.SLS
Retrocopy >GPLGLFTQDLVYHHHHTLLHNGCWLVWLINMGES<LVAMVLCK*KGITNTRPQLLWFLQIFLFGIGSLS

Parental  ILIAYRPKRQKQT
          ILIAYRPK.QK.T
Retrocopy ILIAYRPKCQKHT

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_602 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_602 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_602 has 0 orthologous retrocopies within eutheria group .

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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,