RetrogeneDB ID: retro_cfam_1010

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:18766478..18767556(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000030498
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ENO3
• Ensembl ID: ENSCAFG00000015802
• Aliases: None
• Description: enolase 3 (beta, muscle) [Source:HGNC Symbol;Acc:3354]

Sequence

>retro_cfam_1010
CTAAACCTAACTCTTGCACCTGCCCTGACTAGCAAGAAGTGAACGTTGTGGAGCAGGAAAAGATTGACAAACTGATGATC
GAGATGGACGGGACAGAGAATAAATCTAAATTTGGTGCAAACGCTATTCTGGGAGTGTCCCTGGCTGTCTGCAAGGCAGG
GGCTGTCGAGAAGGAGGTGCCCCCGTACCACCACATTGCTGACTTGGCTGGCAATTCTGAAGTTATCCTGCCAGTTCCGG
CTTTCAATGTCATCAACGGTGGTTCCCATGCTGGCAACAAGCTGGCCGTGCAGGAGTTCATGATCCTTCTCATTGGTACA
GCTAACTTCAAGGAGGACATGCACATGGGGGAGACGATTTATCACAACCTGAAGAATGTCATCAAGAAGAAATAGGGAAA
AGATGCCACCAATGTGGGCGATGAAGGTGGATTTGCTCCTAATATCCTGGAGAACAAAGAAGCTCTGGAACTGCTGAAGA
ATGCCATCGGGAAGGCTGGCTACACCGATAAGGTGGTCACCGCATGGATGTAGCTGCTTCCGAGTTCTTCAGGTCTGGGA
AGTATGACCTGGACTTCAAGTCCCCTGATGACCCCAGAAGGTACATCACTCCTGACCGGCTGGCTGACCTCTACAAGTCC
TTCATCAGGGGCTACCCACTGGTGTCTATCGAAGACCCCTTTGACCAGGATGTCTGGGAAGCTTGGCAGAAGTTCACTGG
AATCCAGGTGGTAGGGGACGATCTCACCGTGACCAACCTGAAGCGGATTTCTGAGGCTGTGGGCGAGAAATCATGCAACT
GCCTCCTGCTTAAAGTGAACCAGATTGGCTCTGTGACCGAGTCTCTTGAGGTGTGCAAGCTGACCCAGTCCAATGGGTGG
GGCGTCATGGTGTCGCATTGCTCCGGGGAGATCGAAGATACCTTCATCGCCGACCTGGTGGTGGGACTCTGCACTGGGCA
GATCAAGACGGGTACACCATGCAGATCCGAGCACTTGGCCAAAGACAACCAGATCCTCAGAACTGAAGAGGAACTGGGTA
GCAAGGCCAAGTTCGCCGGCAGAAGCTTCAGAAACCCC

Alignment

ORF - retro_cfam_1010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.34 %
• Parental protein coverage: 83.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  INKTLGPALLEKK-LSVVDQEKVDKFMIELDGTENKSKFGANAILGVSLAVCKAGAAEKGVPLYRHIADL
          .N.TL.PAL..KK...VV.QEK.DK.MIE.DGTENKSKFGANAILGVSLAVCKAGA.EK.VP.Y.HIADL
Retrocopy LNLTLAPALTSKK<VNVVEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKEVPPYHHIADL

Parental  AGNPDLVLPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFREAMRIGAEVYHHLKGVIKAKYGKDATNV
          AGN....LPVPAFNVINGGSHAGNKLA.QEFMIL..G...F.E.M..G...YH.LK.VIK.K.GKDATNV
Retrocopy AGNSEVILPVPAFNVINGGSHAGNKLAVQEFMILLIGTANFKEDMHMGETIYHNLKNVIKKK*GKDATNV

Parental  GDEGGFAPNILENNEALELLKTAIQAAGYPDKVVIG-MDVAASEFYRNGKYDLDFKSPDDPARHITGEKL
          GDEGGFAPNILEN.EALELLK.AI..AGY.DKVV...MDVAASEF.R.GKYDLDFKSPDDP.R.IT...L
Retrocopy GDEGGFAPNILENKEALELLKNAIGKAGYTDKVVTA<MDVAASEFFRSGKYDLDFKSPDDPRRYITPDRL

Parental  GELYKSFIKNYPVVSIEDPFDQDDWATWTSFLSGVNIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQ
          ..LYKSFI..YP.VSIEDPFDQD.W..W..F.....IQ.VGDDLTVTN.KRI..AV..K.CNCLLLKVNQ
Retrocopy ADLYKSFIRGYPLVSIEDPFDQDVWEAWQKF---TGIQVVGDDLTVTNLKRISEAVGEKSCNCLLLKVNQ

Parental  IGSVTESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEA
          IGSVTES...CKL.QSNGWGVMVSH.SGE.EDTFIADLVVGLCTGQIKTG.PCRSE.LAK.NQ..R.EE.
Retrocopy IGSVTESLEVCKLTQSNGWGVMVSHCSGEIEDTFIADLVVGLCTGQIKTGTPCRSEHLAKDNQILRTEEE

Parental  LGDKAVFAGRKFRNP
          LG.KA.FAGR.FRNP
Retrocopy LGSKAKFAGRSFRNP

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	1.09 RPM	15.88 RPM
SRP017611_brain	1.51 RPM	6.51 RPM
SRP017611_kidney	2.31 RPM	3.30 RPM
SRP017611_liver	0.65 RPM	20.38 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1010 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1010 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1010 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014523	1 retrocopy	retro_cfam_320,
Canis familiaris	ENSCAFG00000015802	2 retrocopies	retro_cfam_1010 , retro_cfam_2134,
Callithrix jacchus	ENSCJAG00000011679	2 retrocopies	retro_cjac_115, retro_cjac_177,
Macropus eugenii	ENSMEUG00000007915	25 retrocopies	retro_meug_1019, retro_meug_1341, retro_meug_1483, retro_meug_1540, retro_meug_1566, retro_meug_1605, retro_meug_170, retro_meug_1701, retro_meug_1743, retro_meug_1869, retro_meug_1905, retro_meug_1929, retro_meug_2026, retro_meug_2190, retro_meug_235, retro_meug_269, retro_meug_578, retro_meug_607, retro_meug_637, retro_meug_803, retro_meug_820, retro_meug_906, retro_meug_965, retro_meug_973, retro_meug_976,