RetrogeneDB ID: retro_amel_286

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192375.1:2227274..2227790(-)
• Located in intron of: ENSAMEG00000008133

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP4C
• Ensembl ID: ENSAMEG00000015223
• Aliases: None
• Description: protein phosphatase 4, catalytic subunit [Source:HGNC Symbol;Acc:9319]

Sequence

>retro_amel_286
GGGGACTTCGTGGATGGCAGTTTCTACAGCGTCAAAACATTCCTCCTGCTGCTGGCACTTAAGGTTCGCTATCCAGACTG
CATCACCTTGATCTGGAGCAACCATGAAAGCCACCAGATCACCCAGGTCTATGGCTTCTACGACGAGTGTCTGAGTAAAT
ATGGCTCAGTAACCATGTGGCGCTACTGCACTGAGATCTTTGATTACCTCAGCCTGTCGGCCATCATTGATGGCAAGATC
TTCTGCATGCACGGGGGTCTCTCCCCATCTATCTACACCTTGGATCAGATCCAGACGATTGATGGAAAGCAAGAGGTGCC
CCACGATGGGCCCATGTGTGACGTGCTCTGGTCTTACCGTGAAGACACAACAGGCTGGGGCGTGAGCCCCCATGAAGCTG
GCTACCTGTTCAGCAGAGACACAGTGACCCAGTTCAACGCAGCCAACGACAGTGATATGATCTGCCGTGCCCACCAACTG
GTGATGGAAGGTTGCCAGTGTCACCTCAATGAGACT

Alignment

ORF - retro_amel_286 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.3 %
• Parental protein coverage: 56.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDFVDRGFYSVETFLLLLALKVRYPDRITLIRGNHESRQITQVYGFYDECLRKYGSVTVWRYCTEIFDYL
          GDFVD..FYSV.TFLLLLALKVRYPD.ITLI..NHES.QITQVYGFYDECL.KYGSVT.WRYCTEIFDYL
Retrocopy GDFVDGSFYSVKTFLLLLALKVRYPDCITLIWSNHESHQITQVYGFYDECLSKYGSVTMWRYCTEIFDYL

Parental  SLSAIIDGKIFCVHGGLSPSIQTLDQIRTIDRKQEVPHDGPMCDLLWSDPEDTTGWGVSPRGAGYLFGSD
          SLSAIIDGKIFC.HGGLSPSI.TLDQI.TID.KQEVPHDGPMCD.LWS..EDTTGWGVSP..AGYLF..D
Retrocopy SLSAIIDGKIFCMHGGLSPSIYTLDQIQTIDGKQEVPHDGPMCDVLWSYREDTTGWGVSPHEAGYLFSRD

Parental  VVAQFNAANDIDMICRAHQLVMEGYKWHFNET
          .V.QFNAAND.DMICRAHQLVMEG...H.NET
Retrocopy TVTQFNAANDSDMICRAHQLVMEGCQCHLNET

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_286 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_286 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001615	1 retrocopy	retro_amel_663,
Ailuropoda melanoleuca	ENSAMEG00000015223	1 retrocopy	retro_amel_286 ,
Canis familiaris	ENSCAFG00000017089	1 retrocopy	retro_cfam_16,
Ciona savignyi	ENSCSAVG00000004266	1 retrocopy	retro_csav_27,
Equus caballus	ENSECAG00000022179	1 retrocopy	retro_ecab_911,
Felis catus	ENSFCAG00000014171	1 retrocopy	retro_fcat_1043,
Macropus eugenii	ENSMEUG00000000397	5 retrocopies	retro_meug_1014, retro_meug_1188, retro_meug_1336, retro_meug_560, retro_meug_859,
Ornithorhynchus anatinus	ENSOANG00000008136	1 retrocopy	retro_oana_25,
Pan troglodytes	ENSPTRG00000007984	1 retrocopy	retro_ptro_28,
Tursiops truncatus	ENSTTRG00000005532	1 retrocopy	retro_ttru_1015,