RetrogeneDB ID: retro_amel_518

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192484.1:304306..305304(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000011042
• Aliases: None
• Description: None

Sequence

>retro_amel_518
AAGTGCTTCTCTATCTATGTTGGCCAGACTGGCGTCCATATCAACAATGCCTGCTGGCAGTTCGGTTGCCTAGAACATGG
CATTCAGCCCAAAGGCCACATGCCAAGTGACAAGACCATTGGGGGAAGAGATGACTCCTTCAGCACCTACTTCAGTGAGA
TGGGTCATGGCAAGCATGTGCCCAGGGCAGTGTTTGTAGACCTGGAACCCACGGTCACGGATGAAGTTTGCACTGGTGCC
TACTGCCAGCTAGTCCACCCTGAACAGCTCATCACAGGCAAGGAAAATGTTGCGAACAATTATGTCCAAGGGCACTACGC
CATTGGCAAGATTGACCATATCTTGGACTAAATTCAGAAACTGGCCAACTAGTTCATAGGTGTTCAGGGTGCTTTGGCTT
TCCACAGCTTTGGAGGGGGAACTGGCTCTGGGTTCACCTCCCTGCTGATGGAACTCTCTATTGATTATGCCAAGAAGTCC
AAGCTGGAGTTCTCCATTTACCCAACTCCCCCCGCCCCCCCAGTTTCTACAGCTGTAGCCGAGCCCTGCAACTCCTCCTC
ACCAGCCACATCACTCTGGAGCACTGTGATTGTGCCCTCATGGTAGACCAGAGGCCGCCTGGGACACTGTTGTAGAATCC
TTGATGTTGAGTGCCCAAACTACATCTGCTTCATTAGCTAGATTGTGTCTTCTATCACTGCGTCCCTCAGGTTTGTTGGA
GCCCTGAATTTGATCTGACAGAATCCCAGACCCACCTGGTACCCTATCCCTGCATCCATTTCCCTCTGGCCACGTAGGCC
CTTGTCATCTCTGCTGAGAAAACCTACCATCAACAGTTCTCTGTAGTAGAGATCACCAATGTGTGCTCTGAGCTGGACAA
CCCGATGGTGAAGTGCGGCCAAGGTAAGAACATGGCTTCCTGCCTGCTGTACCATGGCAATGTGGTTCCTGAAGATATTA
ATGCTGCCATTGCCACCATTAAGACCAAACATCCCGTT

Alignment

ORF - retro_amel_518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.5 %
• Parental protein coverage: 75.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEP
          .C.SI.VGQ.GV.I.NACW...CLEHGIQP.G.MPSDKTIGG.DDSF.T.FSE.G.GKHVPRAVFVDLEP
Retrocopy KCFSIYVGQTGVHINNACWQFGCLEHGIQPKGHMPSDKTIGGRDDSFSTYFSEMGHGKHVPRAVFVDLEP

Parental  TVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIVDLVLDRIRKLADLCTGLQGFLIFHSFG
          TV.DEV.TG.Y.QL.HPEQLITGKE..ANNY..GHY.IGK...D..LD.I.KLA....G.QG.L.FHSFG
Retrocopy TVTDEVCTGAYCQLVHPEQLITGKENVANNYVQGHYAIGK--IDHILD*IQKLAN*FIGVQGALAFHSFG

Parental  GGTGSGFASLLMERLSVDYGKKSKLEFAIYPAPQ---VSTAVVEPYNS-ILTTHTTLEHSDCAFMVDN-E
          GGTGSGF.SLLME.LS.DY.KKSKLEF.IYP......VSTAV.EP.NS..LT.H.TLEH.DCA.MVD..E
Retrocopy GGTGSGFTSLLME-LSIDYAKKSKLEFSIYPTXXXXXVSTAVAEPCNS<LLTSHITLEHCDCALMVDQ<E

Parental  AIYDI-CRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNV-DLTEFQTNLVPYPRIHFPLATYAPV
          A..D..C.R.LD.E.P...N....I..IVSSITASLRF.GALN..DLTE.QT.LVPYP.IHFPLAT.A.V
Retrocopy AAWDT<CCRILDVECP---NYICFIS*IVSSITASLRFVGALNL<DLTESQTHLVPYPCIHFPLAT*ALV

Parental  ISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCMLYRGDVVPKDVNAAIATIKTKRTI
          ISAEK.YH.Q.SV.EITN.C.E..N.MVKC....GK.MA.C.LY.G.VVP.D.NAAIATIKTK...
Retrocopy ISAEKTYHQQFSVVEITNVCSELDNPMVKCG--QGKNMASCLLYHGNVVPEDINAAIATIKTKHPV

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_518 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_518 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006872	4 retrocopies	retro_amel_1162, retro_amel_1367, retro_amel_1387, retro_amel_1895,
Ailuropoda melanoleuca	ENSAMEG00000011042	2 retrocopies	retro_amel_488, retro_amel_518 ,
Equus caballus	ENSECAG00000014403	1 retrocopy	retro_ecab_318,
Felis catus	ENSFCAG00000022091	2 retrocopies	retro_fcat_1375, retro_fcat_647,
Mus musculus	ENSMUSG00000067338	1 retrocopy	retro_mmus_3356,