RetrogeneDB ID: retro_cfam_516

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:32264642..32265650(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000017648
• Aliases: None
• Description: ATP synthase subunit alpha [Source:UniProtKB/TrEMBL;Acc:E2RNG2]

Sequence

>retro_cfam_516
CAAAACGTCAAAACGTCAATTGCTATTGACACAATCATTAATCAGAAACGTTTCAAAGACAGAACTGATGAAAAGAAGAA
GTTATACTGTATTTACGTTGCTGTTCGTCAGAAGAGATTTACGGTTGCCCACTTGGTGAAGAGACTTACAGATGCAGATG
CCATGAAGTACACCCTTGTGGTGTCAGCTACTGCTTCTGATGCTGCTCCACTTGGGTACCTGGCTCCTTATTCTGGCTGT
TCTATGGGAGAGTATTCTAGAGATAATGGCAAACATGCTTTGATCACTTACAATGACTTATTCACACAGGCTGTTGCTTA
TCGTCAGGTGTGTCTGCTGTTCCACCGGCCCCTGGTCGTGAAGCCTATCCAGGTGATGTGTTCTACCTACACTCCCGTCT
GCTACAGAGAGTAGCCAAAATGAACGATTCTTTTGGTGGTGGCTCCTTGACTGCTTTACCAGTCACAGAAACGCAAGCTG
TGATGTGTCTGCTTACATTCCAACAAATGTCATTTCCGTCACTGATGGACAGATCTTGGAAACAGAATTGTTCTACAAAG
GTATCCGCCCTGCCATTAACGTCGGTTTGTCTGTGTCCCATGTTGGATCTGCTGCCCAAACCAGGGCCATGAAGCAGGTG
GCAGGTACCATGAAGCTGGAATTGGCTCAGTATTGTGAGGTTGCTGCTTTTGCCCAGTTGGGTTCTGACCTTGATGCTGC
CACGTAACAACTCTTGAGTCATGCCATGCGATTGACTGAGTTGCTGAAGCAAGGACAGTGTTCTCCCATGGCTATTGAAT
AAGTGACCATTATTTATGCTGGTGTAAGAGGATACCTTGATAAATTGGAGCCCAGCAAGATCACAAAGTTTGAACGTGCT
TTCTTGGCTCATGTTATCAGCCAGCACCAAGCCCTCTTGGGCAATATGAGGGCCGATGGAAAGATCGCGAACAGCCAGAT
GCTAAGCTAAAAGAGATTGTAACAAACTTCTTGGCTGGATTTGAAGCT

Alignment

ORF - retro_cfam_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 61.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAP
          Q..KTSIAIDTIINQKRF.D.TDEKKKLYCIYVA..QKR.TVA.LVKRLTDADAMKYT.VVSATASDAAP
Retrocopy QNVKTSIAIDTIINQKRFKDRTDEKKKLYCIYVAVRQKRFTVAHLVKRLTDADAMKYTLVVSATASDAAP

Parental  LQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRP-PGREAYPGDVFYLHSRLLERAA
          L.YLAPYSGCSMGEY.RDNGKHALI.Y.DL..QAVAYRQ..LL..RP.PGREAYPGDVFYLHSRLL.R.A
Retrocopy LGYLAPYSGCSMGEYSRDNGKHALITYNDLFTQAVAYRQVCLLFHRP<PGREAYPGDVFYLHSRLLQRVA

Parental  KMNDSFGGGSLTALPVIETQA-GDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQ
          KMNDSFGGGSLTALPV.ETQA..DVSAYIPTNVIS.TDGQI.LETELFYKGIRPAINVGLSVS.VGSAAQ
Retrocopy KMNDSFGGGSLTALPVTETQA<CDVSAYIPTNVISVTDGQI-LETELFYKGIRPAINVGLSVSHVGSAAQ

Parental  TRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIYAGV
          TRAMKQVAGTMKLELAQY.EVAAFAQ.GSDLDAAT.QLLS...RLTELLKQGQ.SPMAI.E.V..IYAGV
Retrocopy TRAMKQVAGTMKLELAQYCEVAAFAQLGSDLDAAT*QLLSHAMRLTELLKQGQCSPMAI-E*VTIIYAGV

Parental  RGYLDKLEPSKITKFEHAFLAHVISQHQALLGNIRTDGKIS-EQSDAKLKEIVTNFLAGFEA
          RGYLDKLEPSKITKFE.AFLAHVISQHQALLGN.R.DGKI..EQ.DAKLKEIVTNFLAGFEA
Retrocopy RGYLDKLEPSKITKFERAFLAHVISQHQALLGNMRADGKIA<EQPDAKLKEIVTNFLAGFEA

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	0.13 RPM	394.33 RPM
SRP017611_brain	0.08 RPM	395.22 RPM
SRP017611_kidney	0.07 RPM	1120.78 RPM
SRP017611_liver	0.00 RPM	274.83 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_516 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002507	2 retrocopies	retro_btau_1380, retro_btau_1426,
Canis familiaris	ENSCAFG00000017648	2 retrocopies	retro_cfam_1483, retro_cfam_516 ,
Dasypus novemcinctus	ENSDNOG00000006331	2 retrocopies	retro_dnov_1740, retro_dnov_2525,
Equus caballus	ENSECAG00000021561	1 retrocopy	retro_ecab_788,
Homo sapiens	ENSG00000152234	1 retrocopy	retro_hsap_1702,
Gorilla gorilla	ENSGGOG00000016560	1 retrocopy	retro_ggor_1275,
Macropus eugenii	ENSMEUG00000009770	1 retrocopy	retro_meug_151,
Meleagris gallopavo	ENSMGAG00000009963	1 retrocopy	retro_mgal_14,
Microcebus murinus	ENSMICG00000017500	1 retrocopy	retro_mmur_1210,
Myotis lucifugus	ENSMLUG00000009856	1 retrocopy	retro_mluc_1198,
Macaca mulatta	ENSMMUG00000003570	1 retrocopy	retro_mmul_1208,
Mustela putorius furo	ENSMPUG00000000923	1 retrocopy	retro_mputfur_601,
Nomascus leucogenys	ENSNLEG00000010973	1 retrocopy	retro_nleu_1334,
Oryctolagus cuniculus	ENSOCUG00000003967	1 retrocopy	retro_ocun_1235,
Otolemur garnettii	ENSOGAG00000026684	1 retrocopy	retro_ogar_2623,
Pongo abelii	ENSPPYG00000009130	1 retrocopy	retro_pabe_1363,
Pan troglodytes	ENSPTRG00000009991	1 retrocopy	retro_ptro_1151,
Sarcophilus harrisii	ENSSHAG00000017177	1 retrocopy	retro_shar_109,
Tarsius syrichta	ENSTSYG00000007804	1 retrocopy	retro_tsyr_1186,
Tursiops truncatus	ENSTTRG00000005118	1 retrocopy	retro_ttru_159,