RetrogeneDB ID: retro_cfam_418

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:31225734..31226837(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5DC2
• Ensembl ID: ENSCAFG00000009184
• Aliases: None
• Description: 5'-nucleotidase domain containing 2 [Source:HGNC Symbol;Acc:25717]

Sequence

>retro_cfam_418
GGCCCCCCGGGGCCCGGCGCCCACTGCCCGGGCGCCCTGCACTCTGCGCCCGCCGTTGGTGCCCAACTCAGCGCGCACCT
GTGGGCCTGTCACCAGGACATGAGGAGACTGGTGCACGACCTCCTGCCCCCGGAGGTCTGCAGTCTCCTGAACCCAGCAG
CCATCTATGCCAACAACGAGATAAGCCTGCGTGACGTGGAAGTCTATGGCTGCGACTACGACTACACGCTGGCCCAGGCC
GCAGACGCGCTGCACCCCGAGGTCTTCAGTGCTGCCCGTGGCGTCCTGATGGAGCACTGCTAGCACCCAGAGGGGATCCG
AACTATGACTGCGACCCCAGCTTTGCCATCCCAGGCCTCACAACGACATTCAGAAGAGCCTCCTGATGAAGACCGATGCC
TGCCACTACCTGCAGCTGGGGATGGCCTCCAGGGGCCTCCAGCCTGTGCCTGATGAGGAGGAGGTGCTCAATTTTTATGG
GGGCACCCAGCACACCCCTCTGTACCAGATGAGCGGCTTCTATGGCAAGGGTCCCTCCATCAAGCAGTTCATGGACATCT
TCTCGCTGCCGGAGATGGCGCTGCTGTCCTGCGTGGTAGACCACTTTCGGGGTCACGGCCTGGGGTTTGACCAAGCGCAT
CTCTACAAGGATGTGACGGACGCCATTCGAGACGTGCATGTGAAGGGCCTCGTGTACCCAGTGGATTGAACGGGATATGG
AGAAGTACATCCTGGGAAGCGGACGAGACGTTCGCTGTCCTGAGCCGCCTGGTGGCACATGGGAAACACCTGTTCCTCGT
CACCAACAGCCCTTCCAGCTTCGTGGACAAGGGGATGAGGCACATGGTGGGTCCCGACTGGCGTCGGCTCTTGGACGCGG
TCATCGTCCAGGCTGACAAACCCAGCTTCTTCACTGAGCAGCACAAGCCTTTCAGCAAACTCGATGCGAAGGGCTCCCTG
CGCTGGGGCCGCATCACCCGCCTGGAGAACAGCAAAACCAACCGGCAGGGAAACCTGCAGGGCTCCTGCGCCTGACGGAA
CGGCGGGGACCCCGCGTGCTCTACTCCGGAGACCACCTGTACAGGGACCTGGCGAACATCATC

Alignment

ORF - retro_cfam_418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.7 %
• Parental protein coverage: 66.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GPPGPEAHCPGASHSAPAPAPAGGAELSAHLWARYQDMRRLVHDLLPPEVCSLLNPAAIYANNEISLRDV
          GPPGP.AHCPGA.HS....APA.GA.LSAHLWA..QDMRRLVHDLLPPEVCSLLNPAAIYANNEISLRDV
Retrocopy GPPGPGAHCPGALHS----APAVGAQLSAHLWACHQDMRRLVHDLLPPEVCSLLNPAAIYANNEISLRDV

Parental  EVYGFDYDYTLAQYADALHPEIFSAARDILIEHYKYPEGIR-KYDYDPSFAIRGL-HYDIQKSLLMKIDA
          EVYG.DYDYTLAQ.ADALHPE.FSAAR..L.EH...PEGIR..YD.DPSFAI.GL.H.DIQKSLLMK.DA
Retrocopy EVYGCDYDYTLAQAADALHPEVFSAARGVLMEHC*HPEGIR<NYDCDPSFAIPGL<HNDIQKSLLMKTDA

Parental  FHYVQLGTAYRGLQPVPD-EEVIDLYGGTQHIPLYQMSGFYGKGPSIKQFMDIFSLPEMALLSCVVDHFL
          .HY.QLG.A.RGLQPVPD.EEV...YGGTQH.PLYQMSGFYGKGPSIKQFMDIFSLPEMALLSCVVDHF.
Retrocopy CHYLQLGMASRGLQPVPDEEEVLNFYGGTQHTPLYQMSGFYGKGPSIKQFMDIFSLPEMALLSCVVDHFR

Parental  GHGLEFDQAHLYKDVTDAIRDVHVKGLMY-QWIERDMEKYIL-RGDETFAVLSRLVAHGKQLFLITNSPF
          GHGL.FDQAHLYKDVTDAIRDVHVKGL.Y.QWIERDMEKYIL...DETFAVLSRLVAHGK.LFL.TNSP.
Retrocopy GHGLGFDQAHLYKDVTDAIRDVHVKGLVY>QWIERDMEKYIL>EADETFAVLSRLVAHGKHLFLVTNSPS

Parental  SFVDKGMRHMVGPDWRQLFDVVIVQADKPSFFTDRRKPFRKLDEKGSLHWDRITRLEKGKIYRQGNLY-D
          SFVDKGMRHMVGPDWR.L.D.VIVQADKPSFFT...KPF.KLD.KGSL.W.RITRLE..K..RQGNL...
Retrocopy SFVDKGMRHMVGPDWRRLLDAVIVQADKPSFFTEQHKPFSKLDAKGSLRWGRITRLENSKTNRQGNLQ<G

Parental  FLRLTEWRGPRVLYFGDHLYSDLADLM
          .LRLTE.RGPRVLY.GDHLY.DLA...
Retrocopy LLRLTERRGPRVLYSGDHLYRDLANII

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	1.01 RPM	103.19 RPM
SRP017611_brain	0.24 RPM	9.05 RPM
SRP017611_kidney	0.00 RPM	33.02 RPM
SRP017611_liver	0.00 RPM	8.70 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_418 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_418 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008538	1 retrocopy	retro_amel_278,
Canis familiaris	ENSCAFG00000009184	1 retrocopy	retro_cfam_418 ,
Canis familiaris	ENSCAFG00000010354	1 retrocopy	retro_cfam_684,
Equus caballus	ENSECAG00000015835	1 retrocopy	retro_ecab_805,
Myotis lucifugus	ENSMLUG00000015418	1 retrocopy	retro_mluc_1559,
Tursiops truncatus	ENSTTRG00000008562	1 retrocopy	retro_ttru_1120,