RetrogeneDB ID: retro_amel_1012

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192824.1:567323..567611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNPH1
• Ensembl ID: ENSAMEG00000012390
• Aliases: None
• Description: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 [Source:HGNC Symbol;Acc:21218]

Sequence

>retro_amel_1012
AGGCTCATCCCCGAGCGGGGACCTGGCCCGGCTGCGGCAGACACACGTGGTGGTGGCAGAAGTGACCCAGCCATCGTTGG
GTGTAGGCTATGAGCTGGGCCGGACGTCGCACATAAGCGAATCCTGTGTCTATTCCATCCGAGGCCTGGCTGAGGGTTTC
CAGTCATGATCCCCGGAGCGGCGGACGGCTCGAGGTTCCAGGTGTCGGACTATGAAGAGGGACAGGTGGAGGTCACACTG
GATGGATACTCTGAGGCTGCCGCTCCTTAGGAGGTGGCTGCCTCCCCG

Alignment

ORF - retro_amel_1012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.7 %
• Parental protein coverage: 87.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLIHER-DLAWLQQADVVVAEVTQPSLGVGYELGRA-VALNKRVLCLFRPQSGRVLSAMIRGAADGSRFQ
          RLI.ER.DLA.L.Q..VVVAEVTQPSLGVGYELGR..VA..KR.LCLF.P..G.....MI.GAADGSRFQ
Retrocopy RLIPER>DLARLRQTHVVVAEVTQPSLGVGYELGRT<VA-HKRILCLFHPRPG*GFPVMIPGAADGSRFQ

Parental  VLDYEEGQVEAMLDRYFEADPP-QGAASP
          V.DYEEGQVE..LD.Y.EA..P...AASP
Retrocopy VSDYEEGQVEVTLDGYSEAAAP*EVAASP

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_1012 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1012 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012390	1 retrocopy	retro_amel_1012 ,
Bos taurus	ENSBTAG00000019913	1 retrocopy	retro_btau_518,
Canis familiaris	ENSCAFG00000001837	1 retrocopy	retro_cfam_1148,
Callithrix jacchus	ENSCJAG00000005337	1 retrocopy	retro_cjac_3948,
Equus caballus	ENSECAG00000006660	1 retrocopy	retro_ecab_595,
Felis catus	ENSFCAG00000009722	1 retrocopy	retro_fcat_365,
Homo sapiens	ENSG00000112667	1 retrocopy	retro_hsap_2562,
Nomascus leucogenys	ENSNLEG00000000516	1 retrocopy	retro_nleu_1515,
Pongo abelii	ENSPPYG00000016635	1 retrocopy	retro_pabe_1888,
Pan troglodytes	ENSPTRG00000029662	1 retrocopy	retro_ptro_1493,
Pteropus vampyrus	ENSPVAG00000008743	1 retrocopy	retro_pvam_1400,
Rattus norvegicus	ENSRNOG00000018397	1 retrocopy	retro_rnor_580,
Tursiops truncatus	ENSTTRG00000007022	1 retrocopy	retro_ttru_1520,