RetrogeneDB ID: retro_cfam_442

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:10411568..10412174(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARHGEF39
• Ensembl ID: ENSCAFG00000002073
• Aliases: ARHGEF39, C11H9orf100, C9orf100
• Description: Canis lupus familiaris chromosome 9 open reading frame 100 ortholog (C11H9orf100), mRNA. [Source:RefSeq mRNA;Acc:NM_001195688]

Sequence

>retro_cfam_442
ATGGAGAGGCCAGGCACCAGCGCATGGTGCCAGGTGCAAGAGTAACGCGCCACCTGTTAGGAGGGGAAATGCACCTGCCC
TTCCTGGGAGCTGCTGTAGACAGAGCGGTGCTACCAGGAATAGCTGGGGCTGGTGGCCTCATACTTCATTTGAGTTTTGA
AAGCCAAGAGCATCCTGTGACCAGCAGAACACCAGATCCTGTTTGGGCCCTGGGAGCTCATTTAGAGCACCAGTCAAGAG
CTGCTTCCCTCCCTCCAAGGAGGGCACCTAGGGACAGGGGCTGGAAGTCTTCTGACCCCACCTGGAGTTCTCTATCCAAT
TTGCTGCCAACCGAGAGTGGTCCCAGACCACTCAGTAGGTGCAACTAAAGAAAAACCGTTTCCTGAGCTTTATGCAAGAA
GCTTGGCATGAGTTTAGGAGGCTTCGTCTTAAGATCTGCTTCCCCTGCCTCTGCAGAGGCTCCAGATACTTCTGGCTGAA
ACTTTGGCTGAAAACACAAGTCCCAACAGCCCTAACCACCAGCAGCTCACTTGGGCTGCCTGTTTGATAAGTGAGGCTGC
CCAGAGAATCCACAGCTTTGATTAGAAACAGAAGAATGGCTGGCAC

Alignment

ORF - retro_cfam_442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.22 %
• Parental protein coverage: 61.95 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  METSGAGGRCPVQEQRARW-ERKRTCTARELLQTERRYQEQLGLVATYFVGILRAKGTLRAAERHALFGP
          ME..G....C.VQE.RA...E.K.TC...ELL.TER.YQE.LGLVA.YF...L.AK..L..AE...LFGP
Retrocopy MERPGTSAWCQVQE*RATC*EGKCTCPSWELL*TERCYQE*LGLVASYFI*VLKAKSIL*PAEHQILFGP

Parental  WELIYGASHHPRRDLLPYLEGGHW-GQGLESFCPHLELYTQFAANAEKSRTTLQEQLKKNKRFRRFVRLQ
          WELI...S......LLP.L.GGH..GQGLE.F.PHLE...QFAAN.E.S.TT...QLKKN.RF..F...Q
Retrocopy WELI*STS----QELLPSLQGGHL>GQGLEVF*PHLEFSIQFAANREWSQTTQ*VQLKKN-RFLSF--MQ

Parental  EGRPEFGSLRLQ-DLLPLPLQRLQQYENLVMALAENTVPSSPDHQQLTRAARLISETAQRVHSIGQRQRN
          E...EF..LRL..DLLPLPLQRLQ....L...LAENT.P.SP.HQQLT.AA.LISE.AQR.HS....Q.N
Retrocopy EAWHEFRRLRLK<DLLPLPLQRLQIL--LAETLAENTSPNSPNHQQLTWAACLISEAAQRIHSFD*KQKN

Parental  DQH
          ..H
Retrocopy GWH

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	7.98 RPM
SRP017611_brain	0.00 RPM	3.89 RPM
SRP017611_kidney	0.00 RPM	1.65 RPM
SRP017611_liver	0.00 RPM	0.65 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_442 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_442 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_442 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002073	1 retrocopy	retro_cfam_442 ,
Felis catus	ENSFCAG00000012743	1 retrocopy	retro_fcat_164,