RetrogeneDB ID: retro_cfam_218

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:106657540..106659124(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000003428
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NUP62CL
• Ensembl ID: ENSCAFG00000017963
• Aliases: None
• Description: nucleoporin 62kDa C-terminal like [Source:HGNC Symbol;Acc:25960]

Sequence

>retro_cfam_218
ATGAGTGGGTTTAATTTTGGAGGCACTGGGGCCCCCACAGGTGGGTTCACATTTGGCACTGCAAAGACGGCGACAACCAC
TCCTGCTACTGGGTTTTCTTTCTCTACATCTGGCACTGGTGGGTTTAATTTTGGGACTCCCTCCCAGCCAGCTGCAAGTA
CTCCTTCTACTGGCCTCTTCTCCCTCACAACCCAGGCTCCAGCAACACAAACCCCAGGATTCAGTTTTGGAACCACAACT
CCTGCCACAGGAGGAACTGGATTCTCCTTAGGCATCAGCACACCAAAGCTAAACTTGGGCAGCGTGGCTGCCACCCCAGC
TACAGCACACCCTGGCGGCTTTGGGCTCAGCAGCAGCACCCTCACCAATGCCATCTCGAGCACTGTCACCTCCAGCCAGA
GCACAGCACCCACCGGCTTCATGTTTGGCTCTGCCACCACCTCTGCTGCTCCTTCCACCACACCAGGGGGATTCTCATTC
ACAGCGGGGAGCACGTCCCAGACCGGGACCTCAGGTTTTAATATTGGCTCAATGGGGACTTCAACCCAGCCCACGGCACT
TGCTGGATTGCTCTTCACTCCTGCCACTCCAGCAGCCACTGGAGCGGGAGCCACACAGCCAGCTGCTCCTGCACCCACTG
CTGCCACTACCAGTGCTGGGCCCACACTGTTTGCCTCTCTAGCAACTGCTCCAACCTCATCGACCACCACTGGGCTTTCT
CTTTGTACCCCATCAACCACGGCTGGAACTCCTGGAGCTGGAACACTGGGCTTCAGCTTAAAGGCCACTGGAGCAGCTTC
TACGGCCTCCACAACAACATCCACCACCACGGCCACCACCACCACTGCAGCCACCACTGCAGCCACCACTACCACCACTG
GCTTTGCCTTGAATCTGAAGCCCCTTGCACCGGCCGGGATCACCAGCAATGCACCGGCTGCTGTGGCCGCACCACCTGGC
CCTGGTGCAGCCACTGGGGCATCTACCAGCCCTGTGATGACCTACGCCCAGCTGGAGAGTCTGATCAACAAGTGGAGTCT
GGAGCTGGAGGACCAGGAACGGCACTTCCTGCAGCAGGCCACACAGGTCAATGCCTGGGACCGCACACTGATTGAGAATG
GGGAGAAGATCACTACCCTCCACCGTGAGGTGGAGAAAGTGAAGCTGGACCAGAAGAGGCTGGACCAAGAGCTCGACTTC
ATCCTGTCTCAGCAGAAGGAGTTGGAAGACCTGCTGAGCCCACTGGAGGAGTCGGTCAAGGAGCAGAGTGGCACTGTCTA
CCTGCAGCATGCCGATGAGGAGCGTGAGAAAACCTACAAGCTGGCAGAGAATATCGATGCACAGCTAAAGCGCATGGCCC
AAGACCTCAAGGACATCATCGAGCACTTGAACACATCTGGAGGCCCTGCCGACACCAGCGACCCACTGCAGCAGATCTGC
AAGATCCTCAATGCGCACATGGACTCGCTGCAGTGGATCGACCAGAACTCGGCCCTGTTGCAGAGGAAGGTGGAGGAGGT
GACCAAGGTGTGTGAGGGGCGTCGCAAGGAGCAGGAGCGCAGCTTCCGGATCACATTCGACTGA

Alignment

ORF - retro_cfam_218 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.51 %
• Parental protein coverage: 99.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISGFNFGETGTPSGGFTFGPAKTVTTTSAIGFTFSTPGARGFKFRTLPQPV-STSSTALFSFSNAAPASQ
          .SGFNFG.TG.P.GGFTFG.AKT.TTT.A.GF.FST.G..GF.F.T..QP..ST.ST.LFS....APA.Q
Retrocopy MSGFNFGGTGAPTGGFTFGTAKTATTTPATGFSFSTSGTGGFNFGTPSQPAASTPSTGLFSLTTQAPATQ

Parental  TKPFSFGIP-PATEETGFSLRISAPKLNLGNTCSLIQPAVITGASRLSTSTLTNTLTCSVPSYWVTA-SS
          T..FSFG...PAT..TGFSL.IS.PKLNLG........A...G...LS.STLTN.....V.S...TA...
Retrocopy TPGFSFGTTTPATGGTGFSLGISTPKLNLGSVAATPATAH-PGGFGLSSSTLTNAISSTVTSSQSTAPTG

Parental  FVFGSAITSATESATATGFSFISGSIASNPNMTHFSCWSLIEKAWPTSITPTPSTPSIQLTTVIPSTCLA
          F.FGSA.TSA..S.T..GFSF..GS..S......F...S......PT.......TP.....T....T..A
Retrocopy FMFGSATTSAAPSTTPGGFSFTAGS-TSQTGTSGFNIGSMGTSTQPTALAGLLFTPATPAATGAGATQPA

Parental  SASAADATTCSGTMLFTSTSNASTSAAATGLSFGAPATSMGTFGGITLGFGLKFPGAGGAAHTASTTAST
          ......ATT..G..LF.S...A.TS...TGLS...P.T..GT.G..TLGF.LK...A.GAA.TASTT.ST
Retrocopy APAPTAATTSAGPTLFASLATAPTSSTTTGLSLCTPSTTAGTPGAGTLGFSLK---ATGAASTASTTTST

Parental  TTTTTVTTTTT--TTTTSGFTLNLRSLTSAGINNIVPVGINSLPFT-STVNAIVTPVMTYGQLEGLINKW
          TT.TT.T..TT..TTTT.GF.LNL..L..AGI....P......P.......A...PVMTY.QLE.LINKW
Retrocopy TTATTTTAATTAATTTTTGFALNLKPLAPAGITSNAPAAVAAPPGPGAATGASTSPVMTYAQLESLINKW

Parental  SLDLEDQEKYFLHQATQVNAWDRTLIENGEKITTLHGEVEKVKLDQQRLEQELDFILSQQKELEDLLTPL
          SL.LEDQE..FL.QATQVNAWDRTLIENGEKITTLH.EVEKVKLDQ.RL.QELDFILSQQKELEDLL.PL
Retrocopy SLELEDQERHFLQQATQVNAWDRTLIENGEKITTLHREVEKVKLDQKRLDQELDFILSQQKELEDLLSPL

Parental  EEFVKDQSGSVYLQHADKVHGKTYRLAENIDAQLKRMAQDLKDIIEHLNTFGSPADTTDPLQQICKILNA
          EE.VK.QSG.VYLQHAD....KTY.LAENIDAQLKRMAQDLKDIIEHLNT.G.PADT.DPLQQICKILNA
Retrocopy EESVKEQSGTVYLQHADEEREKTYKLAENIDAQLKRMAQDLKDIIEHLNTSGGPADTSDPLQQICKILNA

Parental  HMDSLQWINQNSVRLKPKIMERKTNAKKQLKKFQQSIYIKF
          HMDSLQWI.QNS..L..K..E.........K....S..I.F
Retrocopy HMDSLQWIDQNSALLQRKVEEVTKVCEGRRKEQERSFRITF

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	29.99 RPM	2.73 RPM
SRP017611_brain	19.85 RPM	0.32 RPM
SRP017611_kidney	15.72 RPM	0.92 RPM
SRP017611_liver	13.34 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_218 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_218 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017963	1 retrocopy	retro_cfam_218 ,
Dasypus novemcinctus	ENSDNOG00000001467	1 retrocopy	retro_dnov_1108,
Felis catus	ENSFCAG00000001984	1 retrocopy	retro_fcat_120,
Macropus eugenii	ENSMEUG00000001005	1 retrocopy	retro_meug_1130,
Nomascus leucogenys	ENSNLEG00000013865	1 retrocopy	retro_nleu_2076,
Pteropus vampyrus	ENSPVAG00000001787	1 retrocopy	retro_pvam_694,
Vicugna pacos	ENSVPAG00000003649	1 retrocopy	retro_vpac_448,