RetrogeneDB ID: retro_cfam_2021

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: JH373239.1:458295..460272(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000004851
• Aliases: None
• Description: None

Sequence

>retro_cfam_2021
ATGGCGGCTCACCTAAAGAAACGAGTGTACGACGAATTCACTAAGGAGGTCCAGCAACAACAGGAGGAAATTGCAACCAA
GAAACTGCGATTGACAAAACCAAGTAAATCTGCAGCACTCCACGTAGATCTGTGTAAAGCTCCCTTCCCAGCGGATGCTT
TGCAGTATCTACTCCAGTTTGCCAGAAAGCCTGTTGAAGCAGAAAGTGTGGAAGGAGTAGTTAGGATTCTCTTGGAACAT
TATTATGGAGAATGATCCATCTGTGAGACTGAAAATTGCATCATTGTTGGGTTTATTATCAAAGACTGCAGGATTTTCAC
CAGACTGCATTATGGATGATGCCAATAACATCCTGCAGAATGAAAAGTCTCATCAAGTCCTTGCTCAACTGTTGGACAGC
TTGCTTGCAACTGGCACCAGACTCCCAGAGAATCAAGCTATCCAGATGGGATTAGTTGATGTAGCCTGCAAGCACCTCAC
AGATACGTCTCATGGTGGAAGAAATAAGTGCCTGCAATTACTTGGCAATCTTGGCTCTTTGGAGAAAAGTGTCACAAAAG
ATGGAGAAGGCCTAGCTGTCAGAGATGTCCAGAAGATGATAGGGGATTACTTCAGTGACCAAGACCCACGTGTCAGAACA
GCAGCTATAAAAGCCATGTTGCAGCTTCATGAGAGAGGACTGAAATTACACCAAGCAATTTATAATCAGGCCTGTAAATT
GTTGTCTGATGACTATGAACAAGGGCGCAGTGCTGCAGTCCAACTTATCTGGGTTGTCAGTCAGCTCTATCCTGAAAGCG
TTGTCTCCATTCCTTCTCCTAATGAAGAAATTCGCTTAGTTGGTGATGCATTTGGAAAAATTTGCCCCATGGTCAATGAT
GGCTCCTGGGTGGTTCGAGTTCAGGCTGCAAAGCTGTTGGGCTCAATGGAACAAGTCAGTTCTCATTTCCTGGAGCAAAC
ACTCGACAAGAAGCTCATGTCCGATCTCAGGAGAAAATGCACTGCACATGAACATGCCAAGGAACTTTACAGGTCAGGAG
AGTTTTCCAGTGGCAGAAAGTGAGGAGGTGATGCTCCCAAAGAAGAAATAGATACAGGAGCTGTGAACTTGATTGAGTCA
GGAGCTTGTGGAGCCTTTGTTCAGGGATTGGAAGATGAGATGTATGAGGTCCTCATTGCTGCTGTGGAGGCTCTCTGCGT
GCTGGCCCAATCTTCACCTTCTTTTGCGGAGAAGTGCCGCCCTGATTTCCTGGTTGACATGTTTAATGATGAAATTGAGG
AAGTACATCTGCAGCCCATACACAGCATGAGAAAAATTTCTAATAATATCACTCTCCGAGAGGATCAGCTTGACACTGTC
CTGGCTGTGTTAGAGGATTCATCCAGAGATATTCGAGAGGCTCTTCATGAACTTTTATGCTGTACTAATGTTTCGACTAA
AGAAGGGATTCATCTTGCACTGGCGGAGCTGCTGAAAAATTTAACCAAGTACCCTACTGATAGGGACTCTATATGGAAGT
GCTTGAAGTTTCTGGGAAGTCGGCATCCAACCCTGGTGCTTCCCTTGGTGCCAGAGCTCCTGAGCACCCATCCGTTTTTT
GACACAGCTGAACCAGACATGGATGAACCAGCTTACATTGCAGTTTTGGTTCTTATTTTTAATGCTGCTAAAACCTGTTC
AACAATGCCAGCACTGTTCTCAGATCATACCTTCAGGCATTATGCCTACCTCTGAGACAGTCTTTCTCATCTTGTTCCTG
CCTTAAGGTTACCAGGTAGAAAACTAGTGTCATCGGCCATTTCTCCCGGTATTGCGCCCCATGAGGACCCGTCCCATCAG
TTCCTGCAGCAGAGCTCTGAAAGGGTGTACAGTCTTCAGAGCACCGGAACCCTCAGGGAACCCAGAAGCTGCTGGAGTTC
ACCATCCAGGATCTTCAAAAACGTGGAGAACTTCAGTCTGAACTAGCAGGAGTCGCT

Alignment

ORF - retro_cfam_2021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.84 %
• Parental protein coverage: 68.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAHLKKRVYEEFTKVVQQQQEEIATKKLRLTKPSKSAALHIDLCKATSPADALQYLLQFARKPVEAESV
          MAAHLKKRVY.EFTK.VQQQQEEIATKKLRLTKPSKSAALH.DLCKA..PADALQYLLQFARKPVEAESV
Retrocopy MAAHLKKRVYDEFTKEVQQQQEEIATKKLRLTKPSKSAALHVDLCKAPFPADALQYLLQFARKPVEAESV

Parental  EGVVRILLEHYY-KENDPSVRLKIASLLGLLSKTAGFSPDCIMDDAINILQNEKSHQVLAQLLDTLLAIG
          EGVVRILLE..Y..ENDPSVRLKIASLLGLLSKTAGFSPDCIMDDA.NILQNEKSHQVLAQLLD.LLA.G
Retrocopy EGVVRILLE-HY>MENDPSVRLKIASLLGLLSKTAGFSPDCIMDDANNILQNEKSHQVLAQLLDSLLATG

Parental  TKLPENQAIQIRLVDVACKHLTDTSHGVRNKCLQLLGNLGSLEKSVTKDGEGLAVRDVQKIIGDYFSDQD
          T.LPENQAIQ..LVDVACKHLTDTSHG.RNKCLQLLGNLGSLEKSVTKDGEGLAVRDVQK.IGDYFSDQD
Retrocopy TRLPENQAIQMGLVDVACKHLTDTSHGGRNKCLQLLGNLGSLEKSVTKDGEGLAVRDVQKMIGDYFSDQD

Parental  PRVRTAAIKAMLQLHERGLKLHQAIYNQACKLLSDDYEQVRSAAVQLIWVVSQLYPESIVPIPSSNEEIR
          PRVRTAAIKAMLQLHERGLKLHQAIYNQACKLLSDDYEQ.RSAAVQLIWVVSQLYPES.V.IPS.NEEIR
Retrocopy PRVRTAAIKAMLQLHERGLKLHQAIYNQACKLLSDDYEQGRSAAVQLIWVVSQLYPESVVSIPSPNEEIR

Parental  LVDDAFGKICHMVSDGSWVVRVQAAKLLGSMEQVSSHFLEQTLDKKLMSDLRRKRTAHERAKELYSSGEF
          LV.DAFGKIC.MV.DGSWVVRVQAAKLLGSMEQVSSHFLEQTLDKKLMSDLRRK.TAHE.AKELY.SGEF
Retrocopy LVGDAFGKICPMVNDGSWVVRVQAAKLLGSMEQVSSHFLEQTLDKKLMSDLRRKCTAHEHAKELYRSGEF

Parental  SSGRKWGDDAPKEEIDTGAVNLIESGACGAFVHGLEDEMYEVRIAAVEALCMLAQSSPSFAEKCL-DFLV
          SSGRK.G.DAPKEEIDTGAVNLIESGACGAFV.GLEDEMYEV.IAAVEALC.LAQSSPSFAEKC..DFLV
Retrocopy SSGRK*GGDAPKEEIDTGAVNLIESGACGAFVQGLEDEMYEVLIAAVEALCVLAQSSPSFAEKCRPDFLV

Parental  DMFNDEIEEVRLQSIHTMRKISNNITLREDQLDTVLAVLEDSSRDIREALHELLCCTNVSTKEGIHLALV
          DMFNDEIEEV.LQ.IH.MRKISNNITLREDQLDTVLAVLEDSSRDIREALHELLCCTNVSTKEGIHLAL.
Retrocopy DMFNDEIEEVHLQPIHSMRKISNNITLREDQLDTVLAVLEDSSRDIREALHELLCCTNVSTKEGIHLALA

Parental  ELLKNLTKYPTDRDSIWKCLKFLGSRHPTLVLPLVPELLSTHPFFDTAEPDMDDPAYIAVLVLIFNAAKT
          ELLKNLTKYPTDRDSIWKCLKFLGSRHPTLVLPLVPELLSTHPFFDTAEPDMD.PAYIAVLVLIFNAAKT
Retrocopy ELLKNLTKYPTDRDSIWKCLKFLGSRHPTLVLPLVPELLSTHPFFDTAEPDMDEPAYIAVLVLIFNAAKT

Parental  CPTMPALFSDHTFRHYAYLRDSLSHLVPALRLPGRKLVSSAVSPSIAPHEDPSHQFLQQSLERVYSLQHL
          C.TMPALFSDHTFRHYAYL.DSLSHLVPALRLPGRKLVSSA.SP.IAPHEDPSHQFLQQS.ERVYSLQ..
Retrocopy CSTMPALFSDHTFRHYAYL*DSLSHLVPALRLPGRKLVSSAISPGIAPHEDPSHQFLQQSSERVYSLQST

Parental  -DPQG-TQELLEFTIRDLQRLGELQSELAGVA
          ..P.G.TQ.LLEFTI.DLQ..GELQSELAGVA
Retrocopy >EPSG>TQKLLEFTIQDLQKRGELQSELAGVA

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	0.04 RPM	22.39 RPM
SRP017611_brain	0.08 RPM	15.32 RPM
SRP017611_kidney	0.00 RPM	10.24 RPM
SRP017611_liver	0.00 RPM	10.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2021 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2021 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2021 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004851	2 retrocopies	retro_cfam_2021 , retro_cfam_2038,