RetrogeneDB ID: retro_amel_633

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192539.1:118568..119082(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000006891
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CIDEB
• Ensembl ID: ENSAMEG00000016089
• Aliases: None
• Description: cell death-inducing DFFA-like effector b [Source:HGNC Symbol;Acc:1977]

Sequence

>retro_amel_633
ATCAAAGCTGCCACATGCCAAGAACTGCTGGACAAGGTGATGGAGACTCCTCAGCTGACTGAAGTGCTAAGAATGGTGCT
AGAGGAAGATGGGACCTCCATGGAGAGCAAGGACTTCTTCCAGCTGTTGGAAGATGACACATGCCTGATGGTGCTAGATT
TTGGGAAAAGCTGGACCCCAGCAGGAATGGGTGCTGTCAAGTGGCCCAGGCCGGGAGAACACCAAGCACAGAAAGGACAT
CACCCTCATCACCTTCAACATATAGAAGCAAAACCCTTGGAACTTCTTTGGCAGCCTAATATCAAAGCCACATTCTACAA
GCTCTACTCCATGAGCTGTGACTCTCAAGGACCTGGTCTAAAGAAAGTACTCAGTGGGCTACTCCACTTGAACCTCCATG
TTGCTGCAAGGCCTGGGCCAAATGTTGCTGGGAATTTCCTCCACCCTTCACCATGCAGTAGAGGGGGCTAAGCAGTGGGA
GCAGCAGCAAAAAGAGGGTGGCCTCCATCCCTAC

Alignment

ORF - retro_amel_633 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.91 %
• Parental protein coverage: 77.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VTAATRQELLDKALEALLLSGMLTLVLEEDGTAVESEDFFQLLEDDTCLMVLECGQSWS-PGRSG-MLSY
          ..AAT.QELLDK..E...L...L..VLEEDGT..ES.DFFQLLEDDTCLMVL..G.SW..P.R.G..LS.
Retrocopy IKAATCQELLDKVMETPQLTEVLRMVLEEDGTSMESKDFFQLLEDDTCLMVLDFGKSWT<PSRNG<VLSS

Parental  GLGREKPKHSKDIARITFDIYKQNPRDLFGSL-NIKATFYGLYSMSCDFQGLGPKKVLRELLRW-TSALL
          G.GRE..KH.KDI..ITF.I.KQNP...FGSL.NIKATFY.LYSMSCD.QG.G.KKVL..LL...TS.LL
Retrocopy GPGRENTKHRKDITLITFNI*KQNPWNFFGSL<NIKATFYKLYSMSCDSQGPGLKKVLSGLLHL>TSMLL

Parental  QGLGHMLLGIASSLRHVVEGAEQW-HWQRQGRLHPY
          QGLG.MLLGI.S.L.H.VEGA.QW...Q..G.LHPY
Retrocopy QGLGQMLLGISSTLHHAVEGAKQWEQQQKEGGLHPY

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_633 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_633 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016089	1 retrocopy	retro_amel_633 ,
Canis familiaris	ENSCAFG00000012240	1 retrocopy	retro_cfam_85,
Equus caballus	ENSECAG00000010495	1 retrocopy	retro_ecab_943,
Felis catus	ENSFCAG00000026821	1 retrocopy	retro_fcat_1418,
Pteropus vampyrus	ENSPVAG00000007036	1 retrocopy	retro_pvam_523,