RetrogeneDB ID: retro_cfam_1418

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:19004779..19005966(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000010412
• Aliases: None
• Description: None

Sequence

>retro_cfam_1418
CCAACCATGAATGAATGCATCTCCATCCACATCGGCCAACCTGGCATGCAAATTGGCAATGCCTGCTGGGAGCTCTATTA
CCTGGAACATTGCATCCAGCCTGACGCTCTAATGCTAAGAGACAAAACCACTGGGAGAGGAGATGACCCCTTCAACACTT
TCTTCAGTGAGAAGAGGTACTGGAAAGCATGTGCCCAGGGCAAAGTTTGTAGACCTGAAACCCATGGTCATTGATGAAGT
TCACATTGGTACCTACTGCCAGCTCTTCCATCCTGAGCAGCTCATCACAAGCAAGGAAGATGCTGCCAATAACTATGCCT
GAGGGCACTACACCATTGGCAAGGAGATCACTGACCTTGTCTTGGGCCAAATTCAGAAACTGGCTGATTGGTGCATAGGT
CTTCAGGGCTTCTTGGTTTTCCACAGCTGGGGAGGGAGAACTGGTTCCAGGTTGATCTTCTGGCTGATGGAATATCTCCC
TGTTGATTACGACAAGAAGTCCAAACTGGAAGTCCCCATTTATTCAGCCCCTCAGGTTTTTAGAGCTGTAACTGAGCCTC
TAATTCCATCCTATCACACCACCCTGGAGCACTCTGACTTTGCCTTCATGGTAGACAATGATGCCATCTGTGACATCTGT
CGTAGAACCTCAATATTGAACTCCCAAACCTACACTAACCTGAATAGGTTGATAGGTCCAATTGTGTCCTCCATCACTCA
AATTAGATGGAGCCCTGATGTTGATTTGATAGAATTCCAGACCAAGCTGGTGCCCTGTCCCCCATCCATTTCCCTCTAGC
CACATATGTGCATGTCATCTCTGCTGAGAAAGCCTACCATTAATAGCTTTCTGTAGCAGAGATTACCAATGCATGCTTTA
AGACAGCCAGTCAGATGGTGAAATGTGACCCTCACCATAGTAAATACGTGGCTTGCTGCCTGTTGTACCATGATGTGGTG
GTTCCCAAAGATATCAGTGCTGCCATTGCCACCATCAAGACCAAGAGTCCATCCAATTTGTGGACTGTTGCCCCACTGGC
TTCAAAGTTGGCATTCATTATCAGCCTTCCACTGTAGTATCTGATAGGGAACTGGCCAAAGTACAAGCTGTGTGCTTGGT
GAGCAATGCCACAGCCATTGCTGAGGCCTGGGTTCACCTAGACTACAAGTTTGATGTATGCCAAGCA

Alignment

ORF - retro_cfam_1418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.17 %
• Parental protein coverage: 77.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PQQHECISIHVGQAGVQMGNTCWELYCLEHSIQPNGTMPSDKALGSGNDSFNTFFSET-GAGKHVPRAIF
          P...ECISIH.GQ.G.Q.GN.CWELY.LEH.IQP...M..DK..G.G.D.FNTFFSE..G.GKHVPRA.F
Retrocopy PTMNECISIHIGQPGMQIGNACWELYYLEHCIQPDALMLRDKTTGRGDDPFNTFFSEK>GTGKHVPRAKF

Parental  VDLEPTVIDGVRTGTYRQLFHPEQLISGKEDAANNYARGHYMVGKEIIDLVLERIRKLTDQCTGLQGFLI
          VDL.P.VID.V..GTY.QLFHPEQLI..KEDAANNYA.GHY..GKEI.DLVL..I.KL.D.C.GLQGFL.
Retrocopy VDLKPMVIDEVHIGTYCQLFHPEQLITSKEDAANNYA*GHYTIGKEITDLVLGQIQKLADWCIGLQGFLV

Parental  FHSFGGGTGSGFTSLLMERLSMDYGKKSKLEFAIYPAPQMSTAVVEPYNSILTTHTTLEHSDCTFMVDNE
          FHS.GG.TGS.....LME.L..DY.KKSKLE..IY.APQ...AV.EP...I...HTTLEHSD..FMVDN.
Retrocopy FHSWGGRTGSRLIFWLMEYLPVDYDKKSKLEVPIYSAPQVFRAVTEPL--IPSYHTTLEHSDFAFMVDND

Parental  AIYDICRNLDI-ERPTYTNVNQLIGQIVSSITASLRFNGALNVDLTEFQTNLVPYP-RIHFPLVTYSPIV
          AI.DICR...I....TYTN.N.LIG.IVSSIT..........VDL.EFQT.LVP.P..IHFPL.TY....
Retrocopy AICDICRRTSILNSQTYTNLNRLIGPIVSSIT---QIRWSPDVDLIEFQTKLVPCP<PIHFPLATYVHVI

Parental  SAEKAYHEQLSVAEITNACFESSNHMVKCDPRHGKYMACCMLYQGEVVPKDVNAAIATIKTK-HSIQFVD
          SAEKAYH..LSVAEITNACF.....MVKCDP.H.KY.ACC.LY...VVPKD..AAIATIKTK..SIQFVD
Retrocopy SAEKAYH**LSVAEITNACFKTASQMVKCDPHHSKYVACCLLYHDVVVPKDISAAIATIKTK<ESIQFVD

Parental  WCPTGFKVGINYQPPTVVPGGDLAKVQQAVCMLSNTTAIAEAWARLNHKFDLMYA
          .CPTGFKVGI.YQP.TVV....LAKV.QAVC..SN.TAIAEAW..L..KFD...A
Retrocopy CCPTGFKVGIHYQPSTVVSDRELAKV-QAVCLVSNATAIAEAWVHLDYKFDVCQA

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	7.90 RPM
SRP017611_brain	0.00 RPM	0.24 RPM
SRP017611_kidney	1.39 RPM	11.56 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1418 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1418 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005248	1 retrocopy	retro_cfam_1124,
Canis familiaris	ENSCAFG00000008640	8 retrocopies	retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463, retro_cfam_926,
Canis familiaris	ENSCAFG00000008661	2 retrocopies	retro_cfam_960, retro_cfam_978,
Canis familiaris	ENSCAFG00000010412	1 retrocopy	retro_cfam_1418 ,