RetrogeneDB ID: retro_amel_1114

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192916.1:1061601..1061854(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf52
• Ensembl ID: ENSAMEG00000002583
• Aliases: None
• Description: chromosome 6 open reading frame 52 [Source:HGNC Symbol;Acc:20881]

Sequence

>retro_amel_1114
CCAGAGTTTCAGCCCCACCAGGGTCACCCCTTTGGCCAACTGGTATGAGAAACAGCACACCTGCTATTCTCTTTCCAGCT
ACAGCTGTGGCTGTGCAGTAAATGGAAATGGACACAACCTTCTTTTTGTGTGTGTGACCTCTGGATACCCAGCTGAAACT
TAGGTTACACTTGAGGAAACCACAGCTCTAGCCAAAAACTGAGATGAAGACCCACCAGAAGATCCACATCTCCATTTGAA
TATTGGGGAATTA

Alignment

ORF - retro_amel_1114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 54.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVFQPCQGYHSD-NWFEQQHSGSSRSVYSCGCAADGNGLN-LSVQETSGRPAETLVTPKESTALAEKQDE
          P.FQP.QG.....NW.E.QH...S.S.YSCGCA..GNG.N.L.V..TSG.PAET.VT..E.TALA...DE
Retrocopy PEFQPHQGHPFG>NWYEKQHTCYSLSSYSCGCAVNGNGHNLLFVCVTSGYPAET*VTLEETTALAKN*DE

Parental  EPLEDPNLHVNIEEL
          .P.EDP.LH.NI.EL
Retrocopy DPPEDPHLHLNIGEL

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_1114 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1114 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 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002583	1 retrocopy	retro_amel_1114 ,
Ailuropoda melanoleuca	ENSAMEG00000011367	1 retrocopy	retro_amel_1782,
Canis familiaris	ENSCAFG00000030234	1 retrocopy	retro_cfam_1098,
Choloepus hoffmanni	ENSCHOG00000010768	2 retrocopies	retro_chof_2530, retro_chof_70,
Equus caballus	ENSECAG00000008229	2 retrocopies	retro_ecab_684, retro_ecab_792,
Monodelphis domestica	ENSMODG00000028324	12 retrocopies	retro_mdom_1372, retro_mdom_2019, retro_mdom_322, retro_mdom_336, retro_mdom_453, retro_mdom_492, retro_mdom_513, retro_mdom_523, retro_mdom_534, retro_mdom_616, retro_mdom_746, retro_mdom_894,
Tursiops truncatus	ENSTTRG00000003650	1 retrocopy	retro_ttru_927,
Vicugna pacos	ENSVPAG00000003001	2 retrocopies	retro_vpac_198, retro_vpac_609,