RetrogeneDB ID: retro_cfam_4

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:7710940..7711366(-)
• Located in intron of: ENSCAFG00000001543

Retrocopy information

• Ensembl ID: ENSCAFG00000029750
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ATP5G3
• Ensembl ID: ENSCAFG00000013366
• Aliases: LOC478807, ATP5G3
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C3 (subunit 9) [Source:HGNC Symbol;Acc:843]

Sequence

>retro_cfam_4
ATGTTTGCCTGCGCCAAGCTCGCTTGCATCCCTGTTCTGATCCGAGCTGGATCCAGAGTTGCATACAGACCAATTTCTGC
ATCATTGTTATATCGACCAGAGGCTAGGACTGGAGAGCACTCTACAGTATTTAATCGGGCCCAGAATGGTGTGCCTCAGC
TAATCCAAAGGGAGTTTCCAACCAGTGCAATCAGGAGAGACATTGATACTGCTGCCAAATTTATTGGTGCAGGTGCTGCA
ACAGTGGGAGTGGCTGGTTCTGGTGCTGGTATTGGAACAGTCTTTGGCAGCTTTATCACTGGTTATGCCAGAAACCCTTT
GCTGAAGCAGCAGCAGTTTTCATATGCTATCCTGGGATTTGCCTTGTCTGAAGCTCTGGGTCTCTTTTGTTTGATGGTTG
CTTTCTTGATTTTGTTTGCTATGTAA

Alignment

ORF - retro_cfam_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLACAKLACAPALIRAGSRVAYRPISASVLYRPEARPGERSTVFNGAQNGVSQRIQREFQTSAISRDIDT
          M.ACAKLAC.P.LIRAGSRVAYRPISAS.LYRPEAR.GE.STVFN.AQNGV.Q.IQREF.TSAI.RDIDT
Retrocopy MFACAKLACIPVLIRAGSRVAYRPISASLLYRPEARTGEHSTVFNRAQNGVPQLIQREFPTSAIRRDIDT

Parental  AAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFA
          AAKFIGAGAATVGVAGSGAGIGTVFGS.I.GYARNP.LKQQ.FSYAILGFALSEA.GLFCLMVAFLILFA
Retrocopy AAKFIGAGAATVGVAGSGAGIGTVFGSFITGYARNPLLKQQQFSYAILGFALSEALGLFCLMVAFLILFA

Parental  M
          M
Retrocopy M

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	0.08 RPM	133.43 RPM
SRP017611_brain	0.00 RPM	80.50 RPM
SRP017611_kidney	0.13 RPM	358.32 RPM
SRP017611_liver	0.07 RPM	79.47 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_4 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_4 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012367	1 retrocopy	retro_amel_1829,
Bos taurus	ENSBTAG00000002944	1 retrocopy	retro_btau_838,
Canis familiaris	ENSCAFG00000013366	2 retrocopies	retro_cfam_4 , retro_cfam_5,
Canis familiaris	ENSCAFG00000016880	5 retrocopies	retro_cfam_1583, retro_cfam_1621, retro_cfam_1882, retro_cfam_336, retro_cfam_647,
Choloepus hoffmanni	ENSCHOG00000012592	3 retrocopies	retro_chof_189, retro_chof_2561, retro_chof_508,
Callithrix jacchus	ENSCJAG00000008207	3 retrocopies	retro_cjac_279, retro_cjac_38, retro_cjac_4183,
Cavia porcellus	ENSCPOG00000006194	1 retrocopy	retro_cpor_479,
Dasypus novemcinctus	ENSDNOG00000010440	2 retrocopies	retro_dnov_235, retro_dnov_396,
Loxodonta africana	ENSLAFG00000010768	1 retrocopy	retro_lafr_120,
Myotis lucifugus	ENSMLUG00000012822	1 retrocopy	retro_mluc_23,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Monodelphis domestica	ENSMODG00000009520	3 retrocopies	retro_mdom_1070, retro_mdom_295, retro_mdom_545,
Mustela putorius furo	ENSMPUG00000013986	1 retrocopy	retro_mputfur_818,
Oryctolagus cuniculus	ENSOCUG00000012164	1 retrocopy	retro_ocun_949,
Otolemur garnettii	ENSOGAG00000027578	1 retrocopy	retro_ogar_1938,
Rattus norvegicus	ENSRNOG00000001596	1 retrocopy	retro_rnor_1106,
Sorex araneus	ENSSARG00000006733	1 retrocopy	retro_sara_82,
Ictidomys tridecemlineatus	ENSSTOG00000013572	4 retrocopies	retro_itri_1091, retro_itri_1236, retro_itri_324, retro_itri_438,
Tupaia belangeri	ENSTBEG00000012159	1 retrocopy	retro_tbel_54,
Tursiops truncatus	ENSTTRG00000011524	3 retrocopies	retro_ttru_268, retro_ttru_510, retro_ttru_588,