RetrogeneDB ID: retro_amel_1548

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193590.1:516416..516761(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000004970
• Aliases: None
• Description: None

Sequence

>retro_amel_1548
GCCACAGAAAGCTGAACTATGGCCATGACCTTGGCTTACTGGGATATCCGTGGGCTGGCTTATACCATCCATCTGCTTCT
GGAACACACAGACGCAAAACTATGAGGAAAAGAAATATGTGATGGGGGTCGCTCCAACTATGACAGAAGCCAGTGGCTGA
ATGAAACATTCAAGTTGAGCCTGGACTTTCAGAACCTGCCCTACTTAATTGATAAAGTTCACAAGATTACCCAGAGCAAT
GCCATCCCTCACTGCATTGCTCACAAACACAACTTATGAGGGGAAACAGAAAAGAAGATTCATGTGGCCATTTTGAAGAA
CTAGGTTCCGGACAACGCCAATCAA

Alignment

ORF - retro_amel_1548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.8 %
• Parental protein coverage: 50.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKRSLTMAMILGYWDIRGLAHAIRLLLEYTDS-HYEEKKYTMGDAP-DYDRSQWLNEKFKLGLDFPNLPY
          A..S.TMAM.L.YWDIRGLA..I.LLLE.TD...YEEKKY.MG.AP..YDRSQWLNE.FKL.LDF.NLPY
Retrocopy ATES*TMAMTLAYWDIRGLAYTIHLLLEHTDA>NYEEKKYVMGVAP<NYDRSQWLNETFKLSLDFQNLPY

Parental  LIDGAHKVTQSNAILRYIARKHNLCGETEEEKIRVDILENQAMDTSNE
          LID..HK.TQSNAI...IA.KHNL.GET.E.KI.V.IL.N...D..N.
Retrocopy LIDKVHKITQSNAIPHCIAHKHNL*GET-EKKIHVAILKN*VPDNANQ

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_1548 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1548 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001020	3 retrocopies	retro_amel_1921, retro_amel_249, retro_amel_778,
Ailuropoda melanoleuca	ENSAMEG00000004970	1 retrocopy	retro_amel_1548 ,
Bos taurus	ENSBTAG00000016472	1 retrocopy	retro_btau_1181,
Canis familiaris	ENSCAFG00000019812	2 retrocopies	retro_cfam_1766, retro_cfam_2062,
Equus caballus	ENSECAG00000024971	1 retrocopy	retro_ecab_1058,
Macaca mulatta	ENSMMUG00000019630	2 retrocopies	retro_mmul_1432, retro_mmul_1806,
Mustela putorius furo	ENSMPUG00000003658	1 retrocopy	retro_mputfur_758,
Mus musculus	ENSMUSG00000027890	1 retrocopy	retro_mmus_204,
Pteropus vampyrus	ENSPVAG00000009559	1 retrocopy	retro_pvam_1047,
Tarsius syrichta	ENSTSYG00000007276	1 retrocopy	retro_tsyr_793,