RetrogeneDB ID: retro_amel_177

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192346.1:1658909..1659252(+)
• Located in intron of: ENSAMEG00000013890

Retrocopy information

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

Parental gene information

• Parental gene symbol: VIMP
• Ensembl ID: ENSAMEG00000007115
• Aliases: None
• Description: VCP-interacting membrane protein [Source:HGNC Symbol;Acc:30396]

Sequence

>retro_amel_177
GCTGTGGAACCTGATGTTGTCGTTAAAGGACAAGAGGCTTGAGCAGCTGCTTGTTTGAAAATGCAAGAGGAATTAAATGC
ACAGGGTAAAAAGTATAAGGAAAAACTAAGACAGCTAGAAGAACAAAAAAAGGAGACAGAACATTGAAATGTGAGACAGT
GTGCAAGAAGGAAAAAGGTACAAAGGAAATGTAAGAAAGCCCCCAGAAGATGAAAGCGCTGGGCTTTCTATTTCATCGGT
CATCCTGAAATGAAAATCTGACAGAAAGCCTTTGCAGGGAGGTGATTACAACCCTTTGCCTGGTGAAGGAAGTGAAGCCT
GCTCCTGGAGACCTGGGCGGAGG

Alignment

ORF - retro_amel_177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.39 %
• Parental protein coverage: 60.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AVDPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLRQLEEQK-RRQKIEMWDSMQEGKSYKGNVRKPPE
          AV.PDVVVK.QEA.AAA.LKMQEELNAQ..K.KEKLRQLEEQK.RRQ.IEM.DS.QEGK.YKGNVRKPPE
Retrocopy AVEPDVVVKGQEA*AAACLKMQEELNAQGKKYKEKLRQLEEQK>RRQNIEM*DSVQEGKRYKGNVRKPPE

Parental  EDGPGPSTSSVLPKRKSDRKPLRGGGYNPLSGEGGGACSWRPGRR
          ....G.S.SSV..K.KSDRKPL.GG.YNPL.GEG..ACSWRPGRR
Retrocopy DESAGLSISSVILK*KSDRKPLQGGDYNPLPGEGSEACSWRPGRR

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_177 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_177 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007115	1 retrocopy	retro_amel_177 ,
Bos taurus	ENSBTAG00000000640	1 retrocopy	retro_btau_1044,
Dasypus novemcinctus	ENSDNOG00000010694	2 retrocopies	retro_dnov_207, retro_dnov_880,
Echinops telfairi	ENSETEG00000011401	1 retrocopy	retro_etel_2096,
Felis catus	ENSFCAG00000028822	1 retrocopy	retro_fcat_1524,
Pteropus vampyrus	ENSPVAG00000012873	1 retrocopy	retro_pvam_1334,