RetrogeneDB ID: retro_amel_498

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192478.1:530201..530686(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD6
• Ensembl ID: ENSAMEG00000008464
• Aliases: None
• Description: programmed cell death 6 [Source:HGNC Symbol;Acc:8765]

Sequence

>retro_amel_498
TTGTGGAGCATTTTCCAGAGGCTTGATAAAGACAGGAGCCAAGTGATATCAGACAACGAGCTTCGGCAAGCACCGTCCAA
AGGCACATGGACTCCACTGAATCCAGTGACTGTCAGGTCAGTCGTATCTATGTTTGACTGAGAGAACAAGGCTGGCATGA
ACTTCAGCAAGTTCAGTGGCACCTGGAAGTACTTCACAGACTGCAGAATGTCTTCCACACCTATGACAGGGACAACTCTG
AGATGATTGACAAGAGCGAGCTAGAGCCAGCTTTCTCAGCGTAACGGCTCTCTGACCAGTTTCATGACATCCTTATTTGA
AAGTTTGACAGACAAGTACAGGGGTAGATCACATTTGATGACTTCATCCAGGGATGCATTCTCTTGCAGGGGTTGACAGA
TATATGCAGACATTATGATAGGGATCAGGATGGCTGAATTCAGGTGTCGTATGAACAGTATCTGTCCGTGGTCTTCGGCA
TTGTA

Alignment

ORF - retro_amel_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.15 %
• Parental protein coverage: 86.77 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LWNVFQRVDKDRSGVISDNELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITD-WQ
          LW..FQR.DKDRS.VISDNEL.QA.S.GTWTP.NPVTVRS..SMFD.ENKAG.NFS.F.G.WKY.TD..Q
Retrocopy LWSIFQRLDKDRSQVISDNELRQAPSKGTWTPLNPVTVRSVVSMFD*ENKAGMNFSKFSGTWKYFTD<LQ

Parental  NVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFR
          NVF.TYDRDNS.MIDK.EL..A.S....RLSDQFHDILI.KFDRQ..G.I.FDDFIQGCI.LQ.LTDI.R
Retrocopy NVFHTYDRDNSEMIDKSELEPAFS--A*RLSDQFHDILI*KFDRQVQG*ITFDDFIQGCILLQGLTDICR

Parental  RYDTDQDGWIQVSYEQYLSMVFSIV
          .YD.DQDG.IQVSYEQYLS.VF.IV
Retrocopy HYDRDQDG*IQVSYEQYLSVVFGIV

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_498 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_498 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008464	1 retrocopy	retro_amel_498 ,
Canis familiaris	ENSCAFG00000011044	2 retrocopies	retro_cfam_1289, retro_cfam_1695,
Felis catus	ENSFCAG00000025521	1 retrocopy	retro_fcat_1800,
Rattus norvegicus	ENSRNOG00000014485	1 retrocopy	retro_rnor_2840,