RetrogeneDB ID: retro_cfam_1483

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:36073231..36074309(+)
• 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_1483
ATTAAGGCCGTGGAGAGCTTGATGCCAATTGCTCATGGTCAGCATGAGCTGATTATTGATGACCGGCAAACTGGCAAAAC
GTCAATTGCTATTGACACAATCATTAATCAGAAATGTTTCAATGACGGGACTGATGAAAAGAAGAAGCTATAGTGTATCT
ATGTCGCTATTGGTCAGAAGAGATCTACGGTTGCCCAGTTGGTGAAGAGACTTACAGATGCAGATGCCATGAAGTTCACC
ATTGTGGTGTCAGCTACTGCTTCTGATGCTGCTCCACTTCGGTGCCTGACTCCTTATTCTGGGGGCGGGGGGGGAGAATA
TTTTAGAGATCATGGCAAACATGCTTTGATCATCTACGATGACTTATCCAGACAGGCTGTTGCTTATCGTTGGATGTCTC
TGCTGCTCCGCCGGCCCCCCGGTCGTGAGGCCTATCCGGGTGATGTGTTCTACCTACATTCCCATCTGCTAGAGAGAGCA
GCCAAAATGAACAATTCTTTTGGTGGTGGCTCCTTGACTGCTTTACCAGTCATAGAAACACAAACTGGTGATGTGAATGC
TTACATTCCGACAGATGTCATTTCCATCACTGATGGACAGATCTTGGGAACAGAATTGTTCTACAAAGGTATCCGCCCTG
CCATTAACGTCAGTTTATCTGTGTCCTGTGTTGGATCTGCTGCCCAAACCAGGGCCATGAGGCAGGTGGCAGGTGCCATG
AAGCTGGAATTGGCTCAGTATTGCGAGACTGCAGCTTTTGCCCAGTTTGGTTCTGACCTTGATGCTGCCACTCAACAACC
CTTGAGTCGTGGCATGAGATTGACTGAGTTGCTGAAGCAAGGATAGTATTTTCCCATGGCTATTGAAGAACAAGTGGCTG
TTATTTATGCTGGTGTAAGAGGATATCTTGATAAATTGGAGCCCAGCAAGATCACAAAGTTTGAGCATGCTTTCTTGGCT
CGTGTTATCAGCCAGCACCAAGCCTTCTTGGACAAATATAAGGACCAATGGAAAGATCTCAGAACAGTCAGATGCTAAGC
TGAAAGAGATTGTAACAAACTTCTTGGCTGGATTTGAA

Alignment

ORF - retro_cfam_1483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.37 %
• Parental protein coverage: 65.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKR
          IKAV.SL.PI..GQ.ELII.DRQTGKTSIAIDTIINQK.FNDGTDEKKKL.CIYVAIGQKRSTVAQLVKR
Retrocopy IKAVESLMPIAHGQHELIIDDRQTGKTSIAIDTIINQKCFNDGTDEKKKL*CIYVAIGQKRSTVAQLVKR

Parental  LTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPP
          LTDADAMK.TIVVSATASDAAPL..L.PYS.....EYFRD.GKHALIIYDDLS.QAVAYR.MSLLLRRPP
Retrocopy LTDADAMKFTIVVSATASDAAPLRCLTPYSXXXXXEYFRDHGKHALIIYDDLSRQAVAYRWMSLLLRRPP

Parental  GREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYK
          GREAYPGDVFYLHS.LLERAAKMN.SFGGGSLTALPVIETQ.GDV.AYIPT.VISITDGQI.L.TELFYK
Retrocopy GREAYPGDVFYLHSHLLERAAKMNNSFGGGSLTALPVIETQTGDVNAYIPTDVISITDGQI-LGTELFYK

Parental  GIRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLK
          GIRPAINV.LSVS.VGSAAQTRAM.QVAG.MKLELAQY.E.AAFAQFGSDLDAATQQ.LSRG.RLTELLK
Retrocopy GIRPAINVSLSVSCVGSAAQTRAMRQVAGAMKLELAQYCETAAFAQFGSDLDAATQQPLSRGMRLTELLK

Parental  QGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFEHAFLAHVISQHQALLG-NIRTDGKISEQSDAKLK
          QG.Y.PMAIEEQVAVIYAGVRGYLDKLEPSKITKFEHAFLA.VISQHQA.L..NIRT.GKISEQSDAKLK
Retrocopy QG*YFPMAIEEQVAVIYAGVRGYLDKLEPSKITKFEHAFLARVISQHQAFLD>NIRTNGKISEQSDAKLK

Parental  EIVTNFLAGFE
          EIVTNFLAGFE
Retrocopy EIVTNFLAGFE

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	0.04 RPM	394.33 RPM
SRP017611_brain	0.00 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_1483 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1483 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1483 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,