RetrogeneDB ID: retro_amel_582

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192511.1:738687..738948(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000011454
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: APOC1
• Ensembl ID: ENSAMEG00000012737
• Aliases: None
• Description: apolipoprotein C-I [Source:HGNC Symbol;Acc:607]

Sequence

>retro_amel_582
AGGCTCATCCTGTTGCTGCTAGTTTTGGCAGTGGTTCTGTGGATGGTTTTGGAAGGCCCAGCTCTGGCCCAGGTAGCCTC
ACAAATCTCCAGAACCTTGGATTGCATCCCTGATAAACTGAAGGAGTTTGGTAATGGCCTGGAGGACAAGGCCCAGGCAG
ATATAGAGAGCATCAAGCAGAGTGACATTCCTGTGAAGACCGGAACTGGTTTTTGGAGACTTTCAACAAAGTGAAGGAGT
GGGTTTAACACTATCTTCTCC

Alignment

ORF - retro_amel_582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.16 %
• Parental protein coverage: 98.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLFLSLSVLVAVLAMVLEGPAPAQAAPEISSTLGSIPDKLKEFGNTLEDKARAAIESIKQSDIPAKT-RN
          RL.L.L.VL..VL.MVLEGPA.AQ.A..IS.TL..IPDKLKEFGN.LEDKA.A.IESIKQSDIP.KT.RN
Retrocopy RLILLLLVLAVVLWMVLEGPALAQVASQISRTLDCIPDKLKEFGNGLEDKAQADIESIKQSDIPVKT<RN

Parental  WFSETFNKVKE-RFKTAFS
          WF.ETFNKVKE..F.T.FS
Retrocopy WFLETFNKVKE>GFNTIFS

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_582 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_582 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012737	1 retrocopy	retro_amel_582 ,
Canis familiaris	ENSCAFG00000004615	1 retrocopy	retro_cfam_530,
Otolemur garnettii	ENSOGAG00000028159	1 retrocopy	retro_ogar_2801,
Rattus norvegicus	ENSRNOG00000018426	1 retrocopy	retro_rnor_204,
Tupaia belangeri	ENSTBEG00000007093	2 retrocopies	retro_tbel_1243, retro_tbel_2226,