RetrogeneDB ID: retro_cfam_1795

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:47433012..47433539(+)
• Located in intron of: ENSCAFG00000019985

Retrocopy information

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

Parental gene information

• Parental gene symbol: SOD2
• Ensembl ID: ENSCAFG00000000671
• Aliases: None
• Description: superoxide dismutase 2, mitochondrial [Source:HGNC Symbol;Acc:11180]

Sequence

>retro_cfam_1795
CTGACTTATGATTATAGTACCCTGGGGTGCCACATTAATGGTCAGAACACACAACTGCACCATAGTAAGCATTGTGTCAA
TTGTATGAATAACTTGAACGCCACTAAGGAGAAATATAAAGAGGACTTGGCAAAAGACAATGTTCTAATTCAGCCTGCAT
TAAAGTTCAGTGGTGGACACCATACCACTCTTAACATTTTAAGAACAATCCTGAGCCCTAATAATGTTGGAGACCACTAA
GGGTGGTTGCTAGAAGCCAGCAAGTGTTACTTTATTTCCTTTGACTTATTTAAGGGGAAGTTGACAGCTGTATCTGTTAG
CATTCACAGTTCAGATTGGAGTTGGCTTGGTTTCATTAAGTAATAAGGACACTTAACAAATTGCTGCCTGTTCTAATCAG
GATCCATTGCAAGGAACAACAGGTCTTATTCCACTTTGGGAGACTGATATATGGTAGTGTGCTTTATTACCTTCAGTATA
AAAGTGTCAGATCTGATTGTCTAAAAGCTGTTTGGAATGCAATCAAC

Alignment

ORF - retro_cfam_1795 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.01 %
• Parental protein coverage: 80.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNTIEEKYLEALEKGDITAQIALQPGLKFNGGGHINHSI
          L.YDY..L..HIN.Q..QLHHSKH.....NNLN...EKY.E.L.K.....Q....P.LKF.GG.H....I
Retrocopy LTYDYSTLGCHINGQNTQLHHSKHCVNCMNNLNATKEKYKEDLAKDNVLIQ----PALKFSGGHHTTLNI

Parental  FWTNLSPKGGGEPKGELLEAIKRDFGSFDKFKEKLTTVSVGVQGSGWGWLGFNKEQGRL-QIAACFNQDP
          ..T.LSP...G...G.LLEA.K..F.SFD.FK.KLT.VSV....S.W.WLGF.K..G.L.QIAAC.NQDP
Retrocopy LRTILSPNNVGDH*GWLLEASKCYFISFDLFKGKLTAVSVSIHSSDWSWLGFIK**GHL>QIAACSNQDP

Parental  LQGTTGLIPLLGIDVWEHA-YYLQYKNVRPDYLKAIWNVIN
          LQGTTGLIPL...D.W..A.YYLQYK.VR.D.LKA.WN.IN
Retrocopy LQGTTGLIPLWETDIW*CA>YYLQYKSVRSDCLKAVWNAIN

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	65.52 RPM
SRP017611_brain	0.00 RPM	85.43 RPM
SRP017611_kidney	0.00 RPM	510.47 RPM
SRP017611_liver	0.00 RPM	128.13 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1795 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1795 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1795 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_840
Callithrix jacchus	retro_cjac_3032

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015466	1 retrocopy	retro_amel_786,
Canis familiaris	ENSCAFG00000000671	1 retrocopy	retro_cfam_1795 ,
Choloepus hoffmanni	ENSCHOG00000003215	4 retrocopies	retro_chof_1952, retro_chof_1966, retro_chof_2620, retro_chof_937,
Callithrix jacchus	ENSCJAG00000011664	1 retrocopy	retro_cjac_3032,
Dasypus novemcinctus	ENSDNOG00000007907	1 retrocopy	retro_dnov_1653,
Equus caballus	ENSECAG00000011797	2 retrocopies	retro_ecab_70, retro_ecab_840,
Echinops telfairi	ENSETEG00000016400	1 retrocopy	retro_etel_731,
Felis catus	ENSFCAG00000002843	1 retrocopy	retro_fcat_1200,
Homo sapiens	ENSG00000112096	1 retrocopy	retro_hsap_430,
Gorilla gorilla	ENSGGOG00000008212	1 retrocopy	retro_ggor_419,
Myotis lucifugus	ENSMLUG00000012242	1 retrocopy	retro_mluc_528,
Monodelphis domestica	ENSMODG00000007521	1 retrocopy	retro_mdom_373,
Mustela putorius furo	ENSMPUG00000005045	1 retrocopy	retro_mputfur_1382,
Nomascus leucogenys	ENSNLEG00000011061	1 retrocopy	retro_nleu_1023,
Otolemur garnettii	ENSOGAG00000017100	1 retrocopy	retro_ogar_1123,
Pongo abelii	ENSPPYG00000017143	1 retrocopy	retro_pabe_292,
Pan troglodytes	ENSPTRG00000018757	1 retrocopy	retro_ptro_327,
Pteropus vampyrus	ENSPVAG00000005302	1 retrocopy	retro_pvam_288,
Rattus norvegicus	ENSRNOG00000019048	1 retrocopy	retro_rnor_2221,
Sarcophilus harrisii	ENSSHAG00000014795	1 retrocopy	retro_shar_210,
Ictidomys tridecemlineatus	ENSSTOG00000008738	1 retrocopy	retro_itri_1432,
Tupaia belangeri	ENSTBEG00000002100	1 retrocopy	retro_tbel_665,
Tarsius syrichta	ENSTSYG00000000457	1 retrocopy	retro_tsyr_183,
Tursiops truncatus	ENSTTRG00000014364	1 retrocopy	retro_ttru_265,