RetrogeneDB ID: retro_amel_366

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192403.1:3002798..3003130(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS8
• Ensembl ID: ENSAMEG00000001217
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 8, 23kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7715]

Sequence

>retro_amel_366
CACTGCGCCGCCATGCATCCATCCATGGGGAGAGGAGAGGAGCGCTGCACCGTGGGCCAGCTCTGCCTGGCGCTCTGCCC
CTACGAGGCCATCACCAGCGAGACCCACGTCACCTGCAGGACCACCCGCTATGACATCGACAAGGCCAAGTGCATCTAGT
GCAGCTGCTACCGGAGGCCCGCCCTGTGGAACACATCGTGAAGGGCCCCAACCTCAAGTTCTCCACGGAGACACAGGAGG
AACTGTTCTACAACGAGGAGACGCAGATCAACAACAAGGCTGAAGGGGAGGCCGAGATCACTGCCAACATCCAGGCCCAC
CACCTCTACCGC

Alignment

ORF - retro_amel_366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.86 %
• Parental protein coverage: 53.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HALRRYPS---GEERCIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCG-FCQEACPVDA
          H.....PS...GEERC....LC.A.CP..AIT.E........R....YDID..KCI.C.....EA.PV..
Retrocopy HCAAMHPSMGRGEERCTVGQLCLALCPYEAITSETHVTCRTTR----YDIDKAKCI*CS<LLPEARPVEH

Parental  IVEGPNFEFSTETHEELLYNKEKLLSNGDKWEAEIAANIQADFLYR
          IV.GPN..FSTET.EEL.YN.E....N....EAEI.ANIQA..LYR
Retrocopy IVKGPNLKFSTETQEELFYNEETQINNKAEGEAEITANIQAHHLYR

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_366 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_366 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001217	2 retrocopies	retro_amel_366 , retro_amel_613,
Canis familiaris	ENSCAFG00000011083	2 retrocopies	retro_cfam_1258, retro_cfam_129,
Callithrix jacchus	ENSCJAG00000015686	4 retrocopies	retro_cjac_1088, retro_cjac_1652, retro_cjac_2237, retro_cjac_3810,
Macropus eugenii	ENSMEUG00000015013	2 retrocopies	retro_meug_1148, retro_meug_926,
Myotis lucifugus	ENSMLUG00000017611	1 retrocopy	retro_mluc_1771,
Mustela putorius furo	ENSMPUG00000004193	1 retrocopy	retro_mputfur_592,
Otolemur garnettii	ENSOGAG00000013220	1 retrocopy	retro_ogar_2669,