RetrogeneDB ID: retro_cfam_325

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:87279883..87280346(-)
• Located in intron of: ENSCAFG00000001880

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1QBP
• Ensembl ID: ENSCAFG00000015542
• Aliases: None
• Description: complement component 1, q subcomponent binding protein [Source:HGNC Symbol;Acc:1243]

Sequence

>retro_cfam_325
ATTGCTGGAGGAAAGATCACTGTCACTTTGAACATTAACATCCTGCCAACATTTCGTGGGGAGGAGGAGCCCTACCAAGG
GCAGAAGGTTAAAAGAACAGCCTGAATTGATGGTCAGCCCTCACTTTTGTGGTTGAAGTTAGAAAGACTGGTGGCAAGAA
AGCCACCAGTGCTGGACTGTCCCTGTCCAGAAGGTGAGGCTGAGCAAGAAGAAGAGGTTGAGAGAGACCTTTTTCTCTAT
GATGGAAGTGAGCTTTCAGCCCATTGTTGAGTCTGAGTGAAAGGATGTGAATTACACACTCAACACTGATCCCCTGGACT
GGGCCTTATGTGAGCACGTGATGGATTTCCTGGCAGACGGATGGGCAGATGACACTTTTGCAGATGAGTTGGTAGAGCTC
AGCACAGCACTGGAGCTTGAGGAACACATCATTTTCCATGAAGATCATAAAGGTTTTGTCAGA

Alignment

ORF - retro_cfam_325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.62 %
• Parental protein coverage: 57.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VAGEKITVTFNINNSIPPTFEGEEEPAQ-GQKADEQEPELTSTPNF-VVEVIKDGGKRAL-VLDCHYPED
          .AG.KITVT.NIN..I.PTF.GEEEP.Q.G....EQ.PEL...P.F.VVEV.K.GGK.A..VLDC..PE.
Retrocopy IAGGKITVTLNIN--ILPTFRGEEEPYQ>GRRLKEQ-PELMVSPHF>VVEVRKTGGKKAT>VLDCPCPEG

Parental  EVGQEEEDESDIF-SIREVSFQAVGESEWKDTNYTLNTDSLDWALYDHLMDFLADRGVDNTFADELVELS
          E..QEEE.E.D.F.S..EVSFQ...ESE.KD.NYTLNTD.LDWAL..H.MDFLAD...D.TFADELVELS
Retrocopy EAEQEEEVERDLF>SMMEVSFQPIVESE*KDVNYTLNTDPLDWALCEHVMDFLADGWADDTFADELVELS

Parental  TALEHQEYITFLEDLKGFVK
          TALE..E.I.F.ED.KGFV.
Retrocopy TALELEEHIIFHEDHKGFVR

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	80.68 RPM
SRP017611_brain	0.00 RPM	59.62 RPM
SRP017611_kidney	0.00 RPM	126.46 RPM
SRP017611_liver	0.00 RPM	46.77 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_325 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_325 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006043	2 retrocopies	retro_amel_1734, retro_amel_356,
Canis familiaris	ENSCAFG00000015542	3 retrocopies	retro_cfam_1595, retro_cfam_319, retro_cfam_325 ,
Felis catus	ENSFCAG00000026474	3 retrocopies	retro_fcat_1135, retro_fcat_1763, retro_fcat_892,
Macropus eugenii	ENSMEUG00000014882	13 retrocopies	retro_meug_1068, retro_meug_1347, retro_meug_1363, retro_meug_1446, retro_meug_1901, retro_meug_1940, retro_meug_1970, retro_meug_2069, retro_meug_2128, retro_meug_434, retro_meug_580, retro_meug_988, retro_meug_989,
Mustela putorius furo	ENSMPUG00000011246	1 retrocopy	retro_mputfur_1213,
Ochotona princeps	ENSOPRG00000013150	1 retrocopy	retro_opri_408,
Sarcophilus harrisii	ENSSHAG00000002441	2 retrocopies	retro_shar_620, retro_shar_813,