RetrogeneDB ID: retro_cfam_1092

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:1920432..1921403(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A16
• Ensembl ID: ENSCAFG00000013726
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; Graves disease autoantigen), member 16 [Source:HGNC Symbol;Acc:10986]

Sequence

>retro_cfam_1092
GCAGTCCTGGCAACAGCCAACTCCCCCTCCCAATGTACCACAGGTGGCAGGACCCAGAGGGCCCACTGCTCACTAGGACT
TCTGGTTGTACTCCTTTCCGGCTAGAGGTATTGCCAGATGCTATGCCAAAACAACAGTTGCTCTTTTGGATTGAGTAAGT
TTTATTACAAACTCACAATCACCATTATATGTATTTAGGAGTATTTTCTGCTTTGTGTGCTATTCCTCAAAAGGAGGGAT
ACCTTTGATTGTATAAAGTGAATGTGCAGTGATGATTTGGATCTTTTTCTACAGTGCAATATAGTTTATGGCATTTGAGC
ATTATAAAATGTTAATTATTATAAAGTTAGGGGTTTATGGCCATGTGCACAGATAAATTGCTGCATCCATGGCAAGTATG
ACAGCAGTTATCTGTACCAATCCTCTTAACATGGTTAGAGTATGCCTAGCATCCCAGGTGAAAGAGGAACATAATTATGC
AAGAATTATTCATGCATTCAAAACAATTTATGCAAATGAAGGTGGTTTTCTTGGATTTTACAGAGGCCTGATGCCTACTA
TGCTAGGAATGGCTCCAAATGCAAGTGTTTCATTTTTATCTTTTGGTACTTTAAAGAGTATTAGGCTTTCCTGTGCTCCT
ACTCTTTTTGGCAGACCTTCATCAGATAATCCTAATGTCTTATTTTTTAAAAACTGATATAAATTTACTTTGTGGTGATG
TTGCTGGAGCAATTGCACAGATCATATCCTATCCATTTGATGTAATTCATTGGCAAAGATAATTAGGAACTATTCTTCCA
GAATCTGAAGAGTATCTTATCATGCGGGAGACTATTAAGTATGTCCATGGACACCATGGAATTTGAGAAGGATTATATTG
TAGTTTATTTCTTAATTACATTTGCTATATTCCATCTCAAACAGTGGCTTTTACAGCATATGACTAGGAAGCAGGTTTTT
GTTACCTCAAC

Alignment

ORF - retro_cfam_1092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.09 %
• Parental protein coverage: 97.89 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AALAAAD-PPPAMPQAAGAGGPAARRDFYWLRSFLAGGIAGCCAKTTVAPLDRVKVLLQA-HNHHYKHLG
          A.LA.A..PPP..PQ.AG..GP.A..DF.WL.SF.A.GIA.C.AKTTVA.LD.V.........H.Y..LG
Retrocopy AVLATAN>PPPNVPQVAGPRGPTAH*DF-WLYSFPARGIARCYAKTTVALLD*VSFITNS>NHH-YMYLG

Parental  VFSALRAVPQKEGYLGLYKGN-GAMMIRIFPYGAIQFMAFEHYKTLITTKLGVSGHVHRLMAGSMAGMTA
          VFSAL.A.PQKEGYL.LYK.N..A.MI.IF.Y.AI.FMAFEHYK.LI..KLGV.GHVHR..A.SMA.MTA
Retrocopy VFSALCAIPQKEGYL*LYKVN<CAVMIWIFFYSAI*FMAFEHYKMLIIIKLGVYGHVHR*IAASMASMTA

Parental  VICTYPLDMVRVRLAFQVKGEHTYTGIIHAFKTIYAKEGGFLGFYRGLMPTILGMAPYAGVSFFTFGTLK
          VICT.PL.MVRV.LA.QVK.EH.Y..IIHAFKTIYA.EGGFLGFYRGLMPT.LGMAP.A.VSF..FGTLK
Retrocopy VICTNPLNMVRVCLASQVKEEHNYARIIHAFKTIYANEGGFLGFYRGLMPTMLGMAPNASVSFLSFGTLK

Parental  SVGLSHAPTLLGRPSSDNPNVL-VLKTHINLLCGGVAGAIAQTISYPFDVTRRRMQLGTALPEFEKCLTM
          S..LS.APTL.GRPSSDNPNVL..LKT.INLLCG.VAGAIAQ.ISYPFDV......LGT.LPE.E..L.M
Retrocopy SIRLSCAPTLFGRPSSDNPNVL>FLKTDINLLCGDVAGAIAQIISYPFDVIHWQR*LGTILPESEEYLIM

Parental  WETMKYVYGHHGIRRGLYRGLSLNYIRCVPSQAVAFTTYELMKQFFHLN
          .ET.KYV.GHHGI..GLY..L.LNYI...PSQ.VAFT.Y.....F..LN
Retrocopy RETIKYVHGHHGI*EGLYCSLFLNYICYIPSQTVAFTAYD*EAGFCYLN

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	13.86 RPM
SRP017611_brain	0.00 RPM	34.69 RPM
SRP017611_kidney	0.07 RPM	40.15 RPM
SRP017611_liver	0.00 RPM	12.54 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1092 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1092 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1092 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013726	1 retrocopy	retro_cfam_1092 ,
Myotis lucifugus	ENSMLUG00000015241	2 retrocopies	retro_mluc_1399, retro_mluc_2012,
Monodelphis domestica	ENSMODG00000017305	1 retrocopy	retro_mdom_1534,
Ochotona princeps	ENSOPRG00000002758	1 retrocopy	retro_opri_1003,
Vicugna pacos	ENSVPAG00000011819	1 retrocopy	retro_vpac_630,