RetrogeneDB ID: retro_amel_523

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192485.1:1018394..1018679(+)
• Located in intron of: ENSAMEG00000010599

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL52
• Ensembl ID: ENSAMEG00000007264
• Aliases: None
• Description: mitochondrial ribosomal protein L52 [Source:HGNC Symbol;Acc:16655]

Sequence

>retro_amel_523
AGGCAGGGCCTGGCTGCCTACCCCTCTGGCTATGGGTCCCATATAGAGTTCCCAAACTGGTCTTATATAGGTGACTGCCC
TGCACTTCCAGTGAAAGGCTAGCTTCGAAGAAAAGCCCAAAAGGAGAAGTTTGCAAGACGAGTTGTACTGCTGTCAGAAT
AAATGGATACTAAATTACAGTCGTGGCAACTTAGGCAGCAGGAGAAGTTGCAGAAGGAAGAAAGGAAGAGAAGAAATGCC
CTTAAACCTGAAGGAGCTCTACTGCAGAACCCACTACCAAGTCAA

Alignment

ORF - retro_amel_523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.68 %
• Parental protein coverage: 77.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQGLAANPSGYGPLTELPDWSYADGRPAPPMKGQLRRKAQREKFARRVVLLSQEMDAGLQAWQLRQQEKL
          .QGLAA.PSGYG...E.P.WSY....PA.P.KG.LRRKAQ.EKFARRVVLLS..MD..LQ.WQLRQQEKL
Retrocopy RQGLAAYPSGYGSHIEFPNWSYIGDCPALPVKG*LRRKAQKEKFARRVVLLSE*MDTKLQSWQLRQQEKL

Parental  QEEERKQKNALKPKGALLQNPRPSQ
          Q.EERK..NALKP.GALLQNP.PSQ
Retrocopy QKEERKRRNALKPEGALLQNPLPSQ

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_523 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_523 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007264	1 retrocopy	retro_amel_523 ,
Bos taurus	ENSBTAG00000014822	1 retrocopy	retro_btau_1839,
Felis catus	ENSFCAG00000006625	1 retrocopy	retro_fcat_1224,
Tupaia belangeri	ENSTBEG00000000986	1 retrocopy	retro_tbel_1871,