RetrogeneDB ID: retro_cfam_2173

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:64772145..64772846(-)
• Located in intron of: ENSCAFG00000017370

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSCAFG00000015855
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_cfam_2173
GCAACCACCCTAGTAGTCACTGGAGGAGCAGACAGCACCAGCCAGTGGTTCAGAGGCTATTACCCCACAGTGGGAAAGCC
AAGAAGTCTCCACAGGGACCACTATCATGGTCAAGCAATTTGACTGGGATGTGGTTCTAGGGGCTAACTCCAGAAAAACC
AAGTTCTACATTGCCAATTGAGTGACTGACAAGCTTACCCCATTCTTGACTGTATTTTCTCCTGCTGCTCAGTCTCAGCA
GCTGATACCCAATCTGTAGCTGATGCTATCACCCATCAGCTTGGTTTCCACAGTATCAAGCTGAATAAAACTTTGCTGGT
ACATAAGGCGGCCAGCCTCTTTAAGGAGATATGTTACTGATACGAAGAAGATCTGATGGTAGGAATCATCATTGTGGGCT
GGGACTTCCAAGAAGGAGGGCAGGTGTACTCAGTGCTCTTGGAGGGTATGATGGTAAGGAAGTCCTTTGCCACTGGGGGC
TTTGGGAGTTCCAGTGTCTATGGTCATGTTGATGCTACCTACTGGGAAGACATGATCAAGGAAGAATGTCAGCAATTCAT
TGCCAATGCTCTTGCTTTGGCCACAGAATGGGTCAGCTCCAGTGGTGGGGTGATCTGCCTATAGCCATTGTAGAATCAGC
GATAGAGCAGCAGGAACTTTTGGAAGATCAGATTCCCAAACTTATCATTGCCACTTTACCA

Alignment

ORF - retro_cfam_2173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.75 %
• Parental protein coverage: 98.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ATLLTARGA-ESAPAWGAEAITPDWESREVSTGTTIMAVQFEGGVVLGADSRTTTGSYIANRVTDKLTP-
          AT.L...G....APA.G.EAITP.WES.EVSTGTTIM..QF...VVLGA.SR.T...YIAN.VTDKLTP.
Retrocopy ATTLVVTGG>QTAPASGSEAITPQWESQEVSTGTTIMVKQFDWDVVLGANSRKTK-FYIAN*VTDKLTP<

Parental  IHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQ
          I.D.IF.C.S.SAADTQ.VADA.T.QLGFHSI.LN...LVH.AASLFKE.CY.Y.EDLM.GIII.GWD.Q
Retrocopy ILDCIFSCCSVSAADTQSVADAITHQLGFHSIKLNKTLLVHKAASLFKEICY*YEEDLMVGIIIVGWDFQ

Parental  EGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVIRL
          EGGQVYSV...GMMVR.SFA.GG.GSS..YG.VDATY.E.M.KEEC.QF.ANALALA.E...SSGGVI.L
Retrocopy EGGQVYSVLLEGMMVRKSFATGGFGSSSVYGHVDATYWEDMIKEECQQFIANALALATEWVSSSGGVICL

Parental  -AAIAESGVERQVLLGDQIPKFTIATLP
          ..AI.ES..E.Q.LL.DQIPK..IATLP
Retrocopy <IAIVESAIEQQELLEDQIPKLIIATLP

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	58.80 RPM
SRP017611_brain	0.00 RPM	30.25 RPM
SRP017611_kidney	0.00 RPM	83.54 RPM
SRP017611_liver	0.00 RPM	27.56 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2173 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2173 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016075	1 retrocopy	retro_amel_1834,
Canis familiaris	ENSCAFG00000015855	1 retrocopy	retro_cfam_2173 ,
Callithrix jacchus	ENSCJAG00000012010	1 retrocopy	retro_cjac_775,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Microcebus murinus	ENSMICG00000014854	2 retrocopies	retro_mmur_140, retro_mmur_718,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Mus musculus	ENSMUSG00000018286	2 retrocopies	retro_mmus_348, retro_mmus_3569,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Tursiops truncatus	ENSTTRG00000000566	1 retrocopy	retro_ttru_405,