RetrogeneDB ID: retro_cfam_891

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:26492173..26493176(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLB
• Ensembl ID: ENSCAFG00000005517
• Aliases: None
• Description: polymerase (DNA directed), beta [Source:HGNC Symbol;Acc:9174]

Sequence

>retro_cfam_891
ATGAGCAAATGGAAGGCACAGCAGCAGACGCTCAATGGGGGAAATCACTAATGTGCTCACAGAACTTGAAAACTATGGGA
AGACCATGAACCAGGCCATCCTCAAGTACAATGCTTACAGAAAAGCAGCATCTGTGATAGCAGAAAACCCATACAAAATA
AAAAGTGGAGCAGAAGCTAAGAAATTGCCTGAAGTAGGAACAAAAAATTGCTGAAAAGATCGATGAATTTTTAGTGACTG
GAAAATTGTGTAAGCTGGAAAAGATCAGCAGGGTGATACGAGTTCCTCTATCAATTTCCTGACTCAAGTTAGTGGCATTG
GTCCATCTGCTGCAAGGAAGTTTGCAGATGAAGGAATTAAAACATTAGAAGATCTCAGAAAAAAATGAAGATATGTTGAA
CCGTCATCAGTGAATTCGGCTGAAATATTTTGAGGAGTTTGAGAAAAGAATTCATCCTGAAGGAATGTTACAAATGTAAG
AAATTATGCTAATGGAATATTAAAAACTGGATTCTGAATTCATTGCTATGGTCTGTGGCAGTTTCCGAAGAGGTGCAGAG
TCTGTTGGTGACATGGATGTTCTGACTCATCCAAACTTTACTTCTGAATCAACCAAATAGCCAAAGCTGTTACATCGTGT
TGTGGAGCAGTTATAGAAGGTCCATTTTATTACAGATGCTCTGTCAAAAGGGGAAACAAAGTTCATTGGTGATTGCCAGC
TTCCCAGTAAAAATGATGAAAAGGAGTATCCACACAGGAGAATTGATAGAAGGTTGCTACCCAAGGATCAATATTACCAT
GGTGTTCTCTATTTCACTAGGAGGATATTTTCAGCAAGAATATGAGTGCTCATCCCCTAGAAAAGGGCTTCCTGATTAAT
GAATACATAGTCCATCCCTGGTGAGTCACTGGAGTTGCTGGAGAACCTCTGCCATGAGTGGATCATGAGAAAGCCATTTT
TGGCTGCGTTCAGTGGAAATACCAAGAACCTAAGGATCAAAGT

Alignment

ORF - retro_cfam_891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.24 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSKRKAPQETLNGG-ITDMLTELANFEKNVNQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGT-K
          MSK.KA.Q.TLNGG.IT..LTEL.N..K..NQAI.KYNAYRKAASVIA..P.KIKSGAEAKKLP.VGT.K
Retrocopy MSKWKAQQQTLNGG>ITNVLTELENYGKTMNQAILKYNAYRKAASVIAENPYKIKSGAEAKKLPEVGT>K

Parental  IAEKIDEFLATGKLRKLEKI-RQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLR-KNEDKLNHHQ
          IAEKIDEFL.TGKL.KLEKI..Q.DTSSSINFLT.VSGIGPSAARKF.DEGIKTLEDLR.KNED.LN.HQ
Retrocopy IAEKIDEFLVTGKLCKLEKI<QQGDTSSSINFLTQVSGIGPSAARKFADEGIKTLEDLR>KNEDMLNRHQ

Parental  RIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESAK
          .I.LKYFE.FEKRI..E.MLQM..I.L.E..K.DSE.IA.VCGSFRRGAES.GDMDV.LTHP.FTSES.K
Retrocopy *IRLKYFEEFEKRIHPEGMLQM*EIMLMEY*KLDSEFIAMVCGSFRRGAESVGDMDV-LTHPNFTSESTK

Parental  QPKLLHRVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTG-S
          .PKLLHRVVEQL.KVHFITD.LSKGETKF.G.CQLPSKNDEKEYPHRRID.RL.PKDQYY.GVLYFT...
Retrocopy *PKLLHRVVEQL*KVHFITDALSKGETKFIGDCQLPSKNDEKEYPHRRIDRRLLPKDQYYHGVLYFTR<E

Parental  DIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP-VDSEKDIFDYIQWKYREPKDRS
          DIF.KNM.AH.LEKGF.INEY...P..VTGVAGEPLP.VD.EK.IF...QWKY.EPKD.S
Retrocopy DIFSKNMSAHPLEKGFLINEYIVHPW*VTGVAGEPLP*VDHEKAIFGCVQWKYQEPKDQS

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	18.65 RPM
SRP017611_brain	0.00 RPM	10.72 RPM
SRP017611_kidney	0.00 RPM	17.24 RPM
SRP017611_liver	0.00 RPM	4.35 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_891 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_891 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005134	1 retrocopy	retro_amel_1482,
Canis familiaris	ENSCAFG00000005517	1 retrocopy	retro_cfam_891 ,
Echinops telfairi	ENSETEG00000002644	1 retrocopy	retro_etel_37,
Macropus eugenii	ENSMEUG00000012619	1 retrocopy	retro_meug_1007,
Procavia capensis	ENSPCAG00000007734	1 retrocopy	retro_pcap_463,