RetrogeneDB ID: retro_cfam_2038

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: JH373600.1:21385..24063(+)
• 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_2038
ATGGCGGCTCACCTAAAGAAACCAGTGTGCGAGGAATTCACTAAGGTGGTCCAGCAACAACAGGAGGAAATTGCAACCAA
GAAACTGCGATTGACAAAACCAAGTAAATCTGCAGCACTCCACGTAGATCGCTGTAAAGCTCCCTCCCCAGCGGATGCTT
TTCAGTATCTACTCCAGTTTGCCAGAAAGCCTTTTGAAGCAGAAAGTGAGGAAGGAGTAGTCAGGATTCTCTTGGAACAT
TGTTACAAGGAGAGTGATCCATCTGTGAGACTGAAAATTGCCTCATTGTTGGGTTTATTATCAAAGACTGCAGGGTTTTC
ACCAGACTGCATTATGGATGATGCCATTAACATCCTGCAGAATGAAAAGTTTCATCACGTCCTTGCTCAACTGTTGGACA
CCTTGCTTGCAATTGGCACCAAACTCCCAGAGAATCAAGCTATCCACATGGGATTAGTTGATGTAGCCTGCAAGCACCTC
ACAGATACATCTCCTGGTGTAAGAAATAAGTGCCTGCAATTACTTGGCAATCTTGGCTCTTTGGAGACAAGTGTCACAAA
AGATGGAGAAGGCCTAGCTCTCAGAGATGTCCAGAAGATTATAGGGGATTACTTCAGTGACCAAGACCCATGTGTCAGAA
GAGCGGCTATAAAAGCCATGTTGCAGCTTCATGAAAGAGGACTGAAATTACACCAAGCAATTTATAATCAGGCCTCTAAA
TTGTTGTCGGATGACTGTGAACAAGTGCGCAGTGCTGCAGTCCAACTTACCTGGGCTATCAGTCAGCTCTATCCTGAAAG
CACTGTCCCCATTCCTTCTTCTAATGAAGAAATTCGCTTAGTTGATGATGCATTTGGAGCAATTTGTCCCATGGTCAGTG
ATGGCTCCTGGGTGGTTCGAGTTCAGGCTGCAAAGCTATTGGGCTCGATGGAACAAGTCAGTTTTCACTTCTTGGAGCAG
ACGCTCGACAAGAAGCTCATGTCAGATCTCAGGAGAAAACGCACTACACATGATTGTACCGAGGAACTTTACAGGTCAGG
AGAGTTAACCAGTGGCTGAATGTGGGGAGGTGATGCTCCCAAAGAAGAAATAGATACAGGAGCTGTGAACTTGATGGAGT
CAGGAGCTTGTGGAGCCTTTGTTCCTGGATTGGAAGATGAGATGTATGAGGTCCGCATTGCTACTTTGGAGGCTCTCTGC
ATGCTGGCCCAATCTTCACCTTCTTTTGCGGAGAAGTGCCGCCCTGATTTCCTGGTGGACATGTTTAATGATGAAATTGA
GGAAGTACGTCTGCAGTCCATACACAGCATGAGAAAAATTTCTAATAATATCACCCTCCGAGAGGATCAGCTTGGCAGTG
TCCTGGCTGTGTTAGAGGATCGTCCAGAGATATTCGAGAGGCTGGCTCTTCACGAACTTTTATGCTGTACTAATGTTTCG
ACTAAAGAAGGGATTCATCTCGCACTGGCGGAGCTGCTGAAAAATTTAACCAAGTACTCTACTGATAGGGACTCTATATG
GAAGTGCTTGAAGTTTCTGGGAAGTCGGCATCCAACCCTGGTGCTTCCCTTGGTGCCAGAGCGCCTGAGCACCCATCCAT
TTTTTGACCCAGCTGAACCAGACATGGATGACCCAGCTTACATTGCAGTTTTGGTTCTTATTTTTAATGCTGCTACAACC
TGTCCAACAATGCCAGCACTATTCTCAGATCATACCTTCAGGCATTATGCCTACCTCCGAGACAGTCTTTCTCATCTTGT
TCCTGCCTTAAGGTTATCAGGTAGAGAACTAGTGTCATCGGCCGTTTCTCCCGGTATTGCGCCCCATGAAGACCCGTCCC
ATCAGTTCCTGCAGCAGAGCCCTGAAAGGGTGTACAGTCTCCAGAGCACCGGGACCCTCAGGGAACCCAGAAGCTGCTGG
AGTTCACCATCCGGGATCTGCAAAGACTTAGAGAACTTCAGTCTGAACTAGCAGGAGTTGCTGACTTCTCGGCTACCTAT
CTTTGGTGTCAGCTTCTTCTCATCAAGGCCTTGCAAGGAAAGCTGTGGAATGTGGCTGCCCCTTTATATTTGAAGCAGAG
TGACTTGGCCTCCGCAGCAGCAAAACAGATCATGGAAGAGACCTACAAAATGGAGTTCATGTACAGTGGTGTGGAGGAGA
AACAGGTGGTGATTATACATCCCATGAGGCTGCAGGCCAAAGCCTTGCAACTTACAGTAACAGCACGGACTACTCGAGGA
GTTGACCCCTTATTTGGGATGTGTGAAAACTTTTTACAGGAAGTGGACTTTTTTCAGAGGTGTTTTATTGCTGATTTGCC
CCCACCTACAGGACAGCTTTGTGGACAAACTTCTTGACCTTATGCCCCGACTCATGACATCCAAGCCTGTGGAAGTGGTC
AAAATTATACAGACCATGCTGAGGCAGAGTACCTCCTTGCACCTCCCCCTTCCAGAGCAGATCCACATACTTCAGCCACC
ATCATTGAGCCAGCAGGCGAGTCAGGCAACCCTTTGCGGTTTACGTCTGGATTGGTTGTGGCCCTGGATGTCGATGCGAC
CCTGGAACATGTGCAGGACCCTGAGAGTGCTGTGAAGGTCCAGGTCTTCTATCCAGATGGCCAGGCTCAGATGATTCATC
CTAAGCCGGCAGACTTGAGGAATCCTGGCCCACCCAGG

Alignment

ORF - retro_cfam_2038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.84 %
• Parental protein coverage: 92.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAHLKKRVYEEFTKVVQQQQEEIATKKLRLTKPSKSAALHIDLCKATSPADALQYLLQFARKPVEAESV
          MAAHLKK.V.EEFTKVVQQQQEEIATKKLRLTKPSKSAALH.D.CKA.SPADA.QYLLQFARKP.EAES.
Retrocopy MAAHLKKPVCEEFTKVVQQQQEEIATKKLRLTKPSKSAALHVDRCKAPSPADAFQYLLQFARKPFEAESE

Parental  EGVVRILLEHYYKENDPSVRLKIASLLGLLSKTAGFSPDCIMDDAINILQNEKSHQVLAQLLDTLLAIGT
          EGVVRILLEH.YKE.DPSVRLKIASLLGLLSKTAGFSPDCIMDDAINILQNEK.H.VLAQLLDTLLAIGT
Retrocopy EGVVRILLEHCYKESDPSVRLKIASLLGLLSKTAGFSPDCIMDDAINILQNEKFHHVLAQLLDTLLAIGT

Parental  KLPENQAIQIRLVDVACKHLTDTSHGVRNKCLQLLGNLGSLEKSVTKDGEGLAVRDVQKIIGDYFSDQDP
          KLPENQAI...LVDVACKHLTDTS.GVRNKCLQLLGNLGSLE.SVTKDGEGLA.RDVQKIIGDYFSDQDP
Retrocopy KLPENQAIHMGLVDVACKHLTDTSPGVRNKCLQLLGNLGSLETSVTKDGEGLALRDVQKIIGDYFSDQDP

Parental  RVRTAAIKAMLQLHERGLKLHQAIYNQACKLLSDDYEQVRSAAVQLIWVVSQLYPESIVPIPSSNEEIRL
          .VR.AAIKAMLQLHERGLKLHQAIYNQA.KLLSDD.EQVRSAAVQL.W..SQLYPES.VPIPSSNEEIRL
Retrocopy CVRRAAIKAMLQLHERGLKLHQAIYNQASKLLSDDCEQVRSAAVQLTWAISQLYPESTVPIPSSNEEIRL

Parental  VDDAFGKICHMVSDGSWVVRVQAAKLLGSMEQVSSHFLEQTLDKKLMSDLRRKRTAHERAKELYSSGEFS
          VDDAFG.IC.MVSDGSWVVRVQAAKLLGSMEQVS.HFLEQTLDKKLMSDLRRKRT.H....ELY.SGE..
Retrocopy VDDAFGAICPMVSDGSWVVRVQAAKLLGSMEQVSFHFLEQTLDKKLMSDLRRKRTTHDCTEELYRSGELT

Parental  SGRKWGDDAPKEEIDTGAVNLIESGACGAFVHGLEDEMYEVRIAAVEALCMLAQSSPSFAEKCL-DFLVD
          SG..WG.DAPKEEIDTGAVNL.ESGACGAFV.GLEDEMYEVRIA..EALCMLAQSSPSFAEKC..DFLVD
Retrocopy SG*MWGGDAPKEEIDTGAVNLMESGACGAFVPGLEDEMYEVRIATLEALCMLAQSSPSFAEKCRPDFLVD

Parental  MFNDEIEEVRLQSIHTMRKISNNITLREDQLDTVLAVLEDSSRDI-REALHELLCCTNVSTKEGIHLALV
          MFNDEIEEVRLQSIH.MRKISNNITLREDQL..VLAVLED......R.ALHELLCCTNVSTKEGIHLAL.
Retrocopy MFNDEIEEVRLQSIHSMRKISNNITLREDQLGSVLAVLEDRPEIFERLALHELLCCTNVSTKEGIHLALA

Parental  ELLKNLTKYPTDRDSIWKCLKFLGSRHPTLVLPLVPELLSTHPFFDTAEPDMDDPAYIAVLVLIFNAAKT
          ELLKNLTKY.TDRDSIWKCLKFLGSRHPTLVLPLVPE.LSTHPFFD.AEPDMDDPAYIAVLVLIFNAA.T
Retrocopy ELLKNLTKYSTDRDSIWKCLKFLGSRHPTLVLPLVPERLSTHPFFDPAEPDMDDPAYIAVLVLIFNAATT

Parental  CPTMPALFSDHTFRHYAYLRDSLSHLVPALRLPGRKLVSSAVSPSIAPHEDPSHQFLQQSLERVYSLQHL
          CPTMPALFSDHTFRHYAYLRDSLSHLVPALRL.GR.LVSSAVSP.IAPHEDPSHQFLQQS.ERVYSLQ..
Retrocopy CPTMPALFSDHTFRHYAYLRDSLSHLVPALRLSGRELVSSAVSPGIAPHEDPSHQFLQQSPERVYSLQST

Parental  -DPQG-TQELLEFTIRDLQRLGELQSELAGVADFSATYLRCQLLLIKALQEKLWNVAAPLYLKQSDLASA
          ..P.G.TQ.LLEFTIRDLQRL.ELQSELAGVADFSATYL.CQLLLIKALQ.KLWNVAAPLYLKQSDLASA
Retrocopy >GPSG>TQKLLEFTIRDLQRLRELQSELAGVADFSATYLWCQLLLIKALQGKLWNVAAPLYLKQSDLASA

Parental  AAKQIMEETYKMEFMYSGVENKQVVIIHHMRLQAKALQLIVTARTTRGVDPLFGMCEKFLQEVDFFQRCF
          AAKQIMEETYKMEFMYSGVE.KQVVIIH.MRLQAKALQL.VTARTTRGVDPLFGMCE.FLQEVDFFQRCF
Retrocopy AAKQIMEETYKMEFMYSGVEEKQVVIIHPMRLQAKALQLTVTARTTRGVDPLFGMCENFLQEVDFFQRCF

Parental  IADL-PHLQDSFVDKLLDLMPRLMTSKPVEVVKILQTMLRQSTFLHLPLPEQIH-KASATIIEPAGESDN
          IADL.PHLQDSFVDKLLDLMPRLMTSKPVEVVKI.QTMLRQST.LHLPLPEQIH...SATIIEPAGES.N
Retrocopy IADL>PHLQDSFVDKLLDLMPRLMTSKPVEVVKIIQTMLRQSTSLHLPLPEQIH<HTSATIIEPAGESGN

Parental  PLRFTSGLVVALDVDATLEHVQDPQSTVKVQVLYPDGQAQMIHPKPADFRNPGPGR
          PLRFTSGLVVALDVDATLEHVQDP.S.VKVQV.YPDGQAQMIHPKPAD.RNPGP.R
Retrocopy PLRFTSGLVVALDVDATLEHVQDPESAVKVQVFYPDGQAQMIHPKPADLRNPGPPR

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	0.46 RPM	22.39 RPM
SRP017611_brain	0.00 RPM	15.32 RPM
SRP017611_kidney	0.00 RPM	10.24 RPM
SRP017611_liver	0.07 RPM	10.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2038 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2038 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 ,