RetrogeneDB ID: retro_ttru_1171

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_106272:62623..63772(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PMPCB
• Ensembl ID: ENSTTRG00000010699
• Aliases: None
• Description: peptidase (mitochondrial processing) beta [Source:HGNC Symbol;Acc:9119]

Sequence

>retro_ttru_1171
TCATTATAATTTGGAGACAACAGATTGAGAAATGCACAAGCCACTATACAAGTTGCTCTGAATGTTCTTGAAACATGAGT
AACATGTTTGGAAAATGAACTCAGAGTGGCCTCTGAAAACTCTGGATTGTCAATATGTACAGTGAGTCTCCGGATTGATG
TTGGAATTTGACATGAAATTAAGAATAATGGAACAGCTCATTCTCTGGAACATATGAACTTCAATGTTACCAAAAAGAGA
TTCAGATTAGATCTGGAACTTGAAAATGAAAACATGGGTGCTCATTTCAACACCTATACCTCCAGAGAGCAGATCATGTA
TTATGCCAAAGAATTCTCTAAAGATTTGCCAAGAGCTGTACGCGTTCTTGCTGATATAACACAAAACAGTACATTGGCAG
AAGCAGAGACTGAGCACAAGTATAGAATAATCCTTAGAGAGATACACGAAATCAAAGCTAATTTACAAGAAGTTGTCTTT
TTATTATCTTAATGTCATAGTTTATCAAATACTGCACTTGGATTGACAATGTGGGGACCAACTGAAAATATCAAATCTAT
AAGTCATAAAGACTTAGTGGACTATATAACCACACATTATAAGAGGCCAAGAATAGTCCTTGCTATGGCTGGAGGAATCT
CCTATAGTGAACAGCTTAAGTTAACAAAGTTTCCTTTTGATGACTTTTTTTTTTTTTTTCCCACACACAAAGGAAAAAGA
ACAACTCTGGCTCCCTGCAAATTCACAGAAAGTGAGATTTGTTTGAGGAATGACAAGATGCCTTTGACACACCTTGCAAG
AGCTGTTCCAGCTGTTGGTTGGGAACATCCTGATACAATCTCTCTCATAGTTGCAAACACACTGACTGGCAACTAGGATT
GCCATTTCAGAGGAGGAATGAATTTAACTAGTAAGCCAGCCTGTCTCATCTGATGTGGCAACCTCTGCCATAGCTTCCAG
TCTTTCAACACTTGCTACACAGATACAGGATTGTGGGGACTCTATATGAGTTGTAAACCAGACATGGCTGCAGGCATGCT
ACATGTTGTTCAAAAAGAATACGTGTGACTCTGTATAAGTGTCACTGAAAGTAAAGTAGCACAAAATCTCTAGAAACAAA
ACATGTTTTTGCACTCTGAGTCAACTCCA

Alignment

ORF - retro_ttru_1171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.87 %
• Parental protein coverage: 84.21 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLYFGGNRLRSTQAATQVVLNVPETHVTCLENGLRVASEDSGLSTCTVGLWIDAGSRYENEKNNGTAHFL
          SL.FG.NRLR..QA..QV.LNV.ET.VTCLEN.LRVASE.SGLS.CTV.L.ID.G...E..KNNGTAH.L
Retrocopy SL*FGDNRLRNAQATIQVALNVLET*VTCLENELRVASENSGLSICTVSLRIDVGI*HEI-KNNGTAHSL

Parental  EHMAFKGTKKRSQLDLELEIENMGAHLNAYTSREQTVYYAKAFSKDLPRAVEILADIIQNSTLGEAEIER
          EHM.F..TKKR..LDLELE.ENMGAH.N.YTSREQ..YYAK.FSKDLPRAV..LADI.QNSTL.EAE.E.
Retrocopy EHMNFNVTKKRFRLDLELENENMGAHFNTYTSREQIMYYAKEFSKDLPRAVRVLADITQNSTLAEAETEH

Parental  ERGVILREMQEVETNLQEVVF-DYLHATAYQ-NTALGRTILGPTENIKSINRKDLVDYITTHYKGPRIVL
          ....ILRE..E...NLQEVVF..YL....YQ.NTALG.T..GPTENIKSI..KDLVDYITTHYK.PRIVL
Retrocopy KYRIILREIHEIKANLQEVVF>YYLNVIVYQ<NTALGLTMWGPTENIKSISHKDLVDYITTHYKRPRIVL

Parental  AAAGGVSHDELLELAKFHFGD---SLSTHKGEIPALPPCKFTGSEIRVRDDKMPLAHLAIAVEAVGWAHP
          A.AGG.S..E.L.L.KF.F.D......THKG....L.PCKFT.SEI..R.DKMPL.HLA.AV.AVGW.HP
Retrocopy AMAGGISYSEQLKLTKFPFDDXXXXXPTHKGKRTTLAPCKFTESEICLRNDKMPLTHLARAVPAVGWEHP

Parental  DTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCHGNLCHSFQSFNTSYTDTGLWGIYMVCEPATVGDML
          DTI.L.VANTL.GN.D..F.GGMNL.SK.A.L...GNLCHSFQSFNT.YTDTGLWG.YM.C.P.....ML
Retrocopy DTISLIVANTLTGN*DCHFRGGMNLTSKPACLI*CGNLCHSFQSFNTCYTDTGLWGLYMSCKPDMAAGML

Parental  HVVQKEWMRLCTSVTESEVARAKNLLKTNMLLQLDGSTP
          HVVQKE...LC.SVTES.V..A.NL.K.NM.L....STP
Retrocopy HVVQKEYV*LCISVTESKV--AQNL*KQNMFLHSE-STP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1171 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1171 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021200	1 retrocopy	retro_cjac_228,
Myotis lucifugus	ENSMLUG00000008798	1 retrocopy	retro_mluc_43,
Rattus norvegicus	ENSRNOG00000012693	1 retrocopy	retro_rnor_2963,
Tursiops truncatus	ENSTTRG00000010699	1 retrocopy	retro_ttru_1171 ,