RetrogeneDB ID: retro_amel_311

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192380.1:1810939..1811541(+)
• Located in intron of: ENSAMEG00000008389

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF13
• Ensembl ID: ENSAMEG00000010433
• Aliases: None
• Description: ring finger protein 13 [Source:HGNC Symbol;Acc:10057]

Sequence

>retro_amel_311
ATGCTGCTTTCTATAGGGATGCTCATTCTGTTGGGCACACAAGTCTATACCATCTTGACTGTCCAGCTCTTTGCATTCTT
AAACCTACTACCTGTAGAAGCAGTATTTTAGCATATAGTTTTGAAAATACATCTAGGATATTTGATGACTTTCCAGTAAG
ATTTGGTTATAGACTTCAAGCTGAAGGTTTAAAGGGTTTTTTGACTAACTCAAAACCAGAGAATGCCTATGAACCCATAA
TGCCTCCACCACTGCAAGACAATTCACTGGCACTTTCATTGTGTTAATTAAAAGACTTGATTGTAATTTCGATGTAAAGG
TTTTAAATGCACAGAGAGCAGGATACGAAGCAGCCATAGTTCACAGTGTTGACTCTGATGACCTCGTTAGCATGGGATCC
AACAACACTGATGTGCTAAATAAATGGACATTCCATCTGTCTTCATTGGGGAATTATCAGCTAATTCCCTGAAAGATGAA
TTCACATATGAAAAAGGGGCCATATTTTCTTAGTTCTAGAATTTAGTCTTCCTTTGGAATGCTACCTAATCCTCTTCTTT
ATTGTAGTGCACATCTGTCTCAGCTTGATAGTCATTTTCATG

Alignment

ORF - retro_amel_311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.55 %
• Parental protein coverage: 53.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLLSIGMLMLSATQVYTILTVQLFAFLNLLPVEA-DILAYNFENASQTFDDLPARFGYRLPAEGLKGFLI
          MLLSIGML.L..TQVYTILTVQLFAFLNLLPVEA..ILAY.FEN.S..FDD.P.RFGYRL.AEGLKGFL.
Retrocopy MLLSIGMLILLGTQVYTILTVQLFAFLNLLPVEA<SILAYSFENTSRIFDDFPVRFGYRLQAEGLKGFLT

Parental  NSKPENACEPIVPPPLKDNS-SGTFIVLIRRLDCNFDVKVLNAQRAGYKAAIVHNVDSDDLISMGSNDID
          NSKPENA.EPI.PPPL.DNS..GTFIVLI.RLDCNFDVKVLNAQRAGY.AAIVH.VDSDDL.SMGSN..D
Retrocopy NSKPENAYEPIMPPPLQDNS<TGTFIVLIKRLDCNFDVKVLNAQRAGYEAAIVHSVDSDDLVSMGSNNTD

Parental  VLKK-IDIPSVFVGESSANSLKDEFTYEKG-GHIILVPEFSLPLEYYLIPFLIIVGICLILIVIFM
          VL.K..DIPSVF.GE.SANSLKDEFTYEKG.GHI.LV.EFSLPLE.YLI.F.I.V.ICL.LIVIFM
Retrocopy VLNK<MDIPSVFIGELSANSLKDEFTYEKG<GHIFLVLEFSLPLECYLILFFIVVHICLSLIVIFM

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_311 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_311 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006392	1 retrocopy	retro_amel_43,
Ailuropoda melanoleuca	ENSAMEG00000010433	1 retrocopy	retro_amel_311 ,
Canis familiaris	ENSCAFG00000008370	1 retrocopy	retro_cfam_815,
Dasypus novemcinctus	ENSDNOG00000014687	1 retrocopy	retro_dnov_139,
Microcebus murinus	ENSMICG00000001221	1 retrocopy	retro_mmur_323,
Nomascus leucogenys	ENSNLEG00000003149	1 retrocopy	retro_nleu_627,
Pongo abelii	ENSPPYG00000014202	1 retrocopy	retro_pabe_2392,