RetrogeneDB ID: retro_amel_1052

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192868.1:804727..805070(-)
• Located in intron of: ENSAMEG00000010617

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM5
• Ensembl ID: ENSAMEG00000013437
• Aliases: None
• Description: phosphoglycerate mutase family member 5 [Source:HGNC Symbol;Acc:28763]

Sequence

>retro_amel_1052
GTCAGCGTGTGGGAGCGGAACCTGGAGTCTGGAGAGAACTGGGGTCCCAGGCTGGACCACTACAAAGGCAAGGCCGTGCA
GCCCATCTTCCTCATCAGGTACTCCCAGTACCGCATGGACGCCTCTTCCCAAAAGGATTTTACTACCGACTCCCCTAGGT
GGCAAACGGGCGAAGCTAACTGGTGTCGGACTTGCAAGCTCGTCGTTGAAGCTTAAAATTGAGCATTCCTGCATGACCCA
AGCAATAGAAACCGCTGACATCATCAGCAAACACATGCCAGGGGCCTGCAAAGTCGGCACAGACTTGCTGAGGGAAGGCG
CCCCCATCTAGCCTAAGGATCCC

Alignment

ORF - retro_amel_1052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.25 %
• Parental protein coverage: 51.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VNLRKRNLDSGEEELASRLDHCKAKATRHIFLIRHSQYHVDASLEKDRTL-TPLGREQAELTGLRLASLG
          V....RNL.SGE.....RLDH.K.KA...IFLIR.SQY..DAS..KD.T..TPLG...A.LTG..LAS..
Retrocopy VSVWERNLESGEN-WGPRLDHYKGKAVQPIFLIRYSQYRMDASSQKDFTT>TPLGGKRAKLTGVGLASSS

Parental  LKFNKIVHSSMTRAIETTDIISKHLPGVCKVSTDLLREGAPIEPDPP
          LK..KI.HS.MT.AIET.DIISKH.PG.CKV.TDLLREGAPI.P..P
Retrocopy LKL-KIEHSCMTQAIETADIISKHMPGACKVGTDLLREGAPI*PKDP

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_1052 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1052 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013437	2 retrocopies	retro_amel_1052 , retro_amel_173,
Choloepus hoffmanni	ENSCHOG00000011867	2 retrocopies	retro_chof_1762, retro_chof_2590,
Felis catus	ENSFCAG00000002503	2 retrocopies	retro_fcat_800, retro_fcat_960,
Homo sapiens	ENSG00000247077	1 retrocopy	retro_hsap_3363,
Myotis lucifugus	ENSMLUG00000013646	1 retrocopy	retro_mluc_1270,
Macaca mulatta	ENSMMUG00000015466	1 retrocopy	retro_mmul_2101,
Mustela putorius furo	ENSMPUG00000002639	1 retrocopy	retro_mputfur_684,
Pan troglodytes	ENSPTRG00000005657	1 retrocopy	retro_ptro_2286,
Rattus norvegicus	ENSRNOG00000037443	1 retrocopy	retro_rnor_1597,
Sus scrofa	ENSSSCG00000026764	1 retrocopy	retro_sscr_821,
Tursiops truncatus	ENSTTRG00000010653	1 retrocopy	retro_ttru_208,