RetrogeneDB ID: retro_amel_309

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192379.1:2518318..2518676(-)
• Located in intron of: ENSAMEG00000004446

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORAOV1
• Ensembl ID: ENSAMEG00000001983
• Aliases: None
• Description: oral cancer overexpressed 1 [Source:HGNC Symbol;Acc:17589]

Sequence

>retro_amel_309
TTTCATAGGGAAGGGTATCAGGAAGGCTATGAAGAAGGCAGTAGTTTGGGTGTAAATGGAGGAAGACAAAATGGCACATT
ACATAGAGTTAAGCTTGGATCTGAGATCAAGGGCTACCAAAATTTTGCTTTTGCCTGGAGAGGTCTCCTACACAGTTGTG
CCACTGAGGAAGACAGCAAAAAGATGAAAGTCTTAGAATCACTAACTGGAATAATTCACAAATTCCCTTATGATCACCCT
GCTTACAATAAACTTCATGAAGACTTAGACAAAAATAAAAGGTAAATTTAAACAGCTTTGTTCATTATTAAATGTTCAGT
TGGACTTTAAAATTAGTGAAGATTCCAGACTTTCATTT

Alignment

ORF - retro_amel_309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FHGEGYQEGYEEGNSLGIIEGRQYGTLHGAKIGSEIGCYQGFAFTWRCLLHSCATEKDSKKMKALESLIG
          FH.EGYQEGYEEG.SLG...GRQ.GTLH..K.GSEI..YQ.FAF.WR.LLHSCATE.DSKKMK.LESL.G
Retrocopy FHREGYQEGYEEGSSLGVNGGRQNGTLHRVKLGSEIKGYQNFAFAWRGLLHSCATEEDSKKMKVLESLTG

Parental  MIQKFPYDDPTYDKLHEDLD-KIRGKFKQLCSLLNVQPDFKISAEGSGLSF
          .I.KFPYD.P.Y.KLHEDLD.KI.GKFKQLCSLLNVQ.DFKIS.E.S.LSF
Retrocopy IIHKFPYDHPAYNKLHEDLD>KIKGKFKQLCSLLNVQLDFKIS-EDSRLSF

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_309 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_309 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001983	1 retrocopy	retro_amel_309 ,
Felis catus	ENSFCAG00000026606	1 retrocopy	retro_fcat_1023,
Homo sapiens	ENSG00000149716	1 retrocopy	retro_hsap_3131,
Microcebus murinus	ENSMICG00000003061	1 retrocopy	retro_mmur_410,
Tursiops truncatus	ENSTTRG00000017307	6 retrocopies	retro_ttru_1122, retro_ttru_1249, retro_ttru_1408, retro_ttru_1785, retro_ttru_272, retro_ttru_860,