RetrogeneDB ID: retro_cfam_771

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:13574458..13575478(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS6KB1
• Ensembl ID: ENSCAFG00000017679
• Aliases: None
• Description: ribosomal protein S6 kinase, 70kDa, polypeptide 1 [Source:HGNC Symbol;Acc:10436]

Sequence

>retro_cfam_771
AGAAAGAGAATATTTATGGAAGACACAGCCTGCTTTTACTTGGCAGAAATCTCCAGGGCTTTGGGGCATTTACATCAAAA
GGGGATTATCTACAGAGACCCGAAGCTGGGGAATATCATACTTAATCATCAAGGTCATGTGAAACTAACAGACTTTGGAT
TATGTAAAGAATCTGTTCACGATGGAACAGTCACACACACATTTTATGGAACAATAGAATACATGCCCCGGAAGTTTTAA
TGAGAAGTGGCCACAATCGTGCTGTGGATTGGTAGAGTTTGGGAACATTCATGCATGACCTGCTGACTGGAGCACCCCCG
ATCACTAGGGAGGATGGAAAGAAAAACGATTGGCAAAATCCTCAAAAGTACATTCAATTTGCCTCTCTACCTCACACAAG
AAGCCAGAGATCTGCTTAAAAAGCTTCTGAAAAGAAATGTTGCTTCTTGGCTTGGAGCTGGTCCTGGGGATGCTGGAGAA
GTTCAAGCTCATCCGTTCTTTGGGCATATAAACCAGGAAGAACTACTGGCTCAGAAGGTAGAGCCCCCTCCTTTAAACCT
CTGTTGCAAGCTGAAGAGGATGTGAGTCAGTTTCATTCAAAGTTTACACATCAGACACCTGTTGACAGCCCAGATGACTC
AACTCTCAGTGAAAGTGCCAACCAGGTCTTTCGGGGGTTTACATATGTGGCTCCATCTGTACTTGAAAGTGTGAAAGAAA
AATTTCCCTTTGAACCAAAAATCTGATCATCTTGATTTATTGGCAGCCCACAAGCACCTGTCAGCCGGGTCAAATCTTCT
CCTGGGGATTTCTGAGGAATGGGCGCTTCAGCCAGCATGGCAAATCCTCAGATACCTGTGGAGTATCCAATGGAAACAAG
TGGAGTAGAGCAAGTGGATGTGACAATGAGTGGGGAAGCTCCAACCCCACTTCCAATATGACAGCTGAACTCCAGGCCAT
ACAAAAAAACAAGCTTTTCCCATGATCTCCAAATGACCAGAGCACCTATATATGAATCTC

Alignment

ORF - retro_cfam_771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.9 %
• Parental protein coverage: 64.76 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  REGIFMEDTACFYLAEISMALGHLHQKGIIYRDLKPENIMLNHQGHVKLTDFGLCKESIHDGTVTHTFCG
          R..IFMEDTACFYLAEIS.ALGHLHQKGIIYRD.K..NI.LNHQGHVKLTDFGLCKES.HDGTVTHTF.G
Retrocopy RKRIFMEDTACFYLAEISRALGHLHQKGIIYRDPKLGNIILNHQGHVKLTDFGLCKESVHDGTVTHTFYG

Parental  TIEYM-APEILMRSGHNRAVDWWSLGALMYDMLTGAPPFTGENRKK-TIDKILKCKLNLPPYLTQEARDL
          TIEYM.APE.LMRSGHNRAVDW.SLG..M.D.LTGAPP.T.E..KK.TI.KILK...NLP.YLTQEARDL
Retrocopy TIEYM<APEVLMRSGHNRAVDW*SLGTFMHDLLTGAPPITREDGKK>TIGKILKSTFNLPLYLTQEARDL

Parental  LKKLLKRNAASRLGAGPGDAGEVQAHPFFRHINWEELLARKVE-PP-FKPLLQSEEDVSQFDSKFTRQTP
          LKKLLKRN.AS.LGAGPGDAGEVQAHPFF.HIN.EELLA.KVE.PP.FKPLLQ.EEDVSQF.SKFT.QTP
Retrocopy LKKLLKRNVASWLGAGPGDAGEVQAHPFFGHINQEELLAQKVEPPP<FKPLLQAEEDVSQFHSKFTHQTP

Parental  VDSPDDSTLSESANQVFLGFTYVAPSVLESVKEKFSFEPKIRSPRRFIGSPRTPVSPVKFSPGDFWGRGA
          VDSPDDSTLSESANQVF.GFTYVAPSVLESVKEKF.FEPKI.S...FIGSP..PVS.VK.SPGDF.G.GA
Retrocopy VDSPDDSTLSESANQVFRGFTYVAPSVLESVKEKFPFEPKI*S-S*FIGSPQAPVSRVKSSPGDF*GMGA

Parental  SASTANPQTPVEYPMETSGVEQMDVTMSGEASAPLPIRQPNSGPY-KKQAFPMISKRPEHLRMNL
          SAS.ANPQ.PVEYPMETSGVEQ.DVTMSGEA..PLPI.Q.NS.PY.KKQAFPMISK.PEHL.MNL
Retrocopy SASMANPQIPVEYPMETSGVEQVDVTMSGEAPTPLPI*QLNSRPY>KKQAFPMISK*PEHLYMNL

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	19.95 RPM
SRP017611_brain	0.00 RPM	15.72 RPM
SRP017611_kidney	0.00 RPM	16.11 RPM
SRP017611_liver	0.00 RPM	12.25 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_771 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_771 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017679	1 retrocopy	retro_cfam_771 ,
Monodelphis domestica	ENSMODG00000014313	2 retrocopies	retro_mdom_1502, retro_mdom_819,