RetrogeneDB ID: retro_amel_1892

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195295.1:30690..31404(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000004755
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSAMEG00000018466
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]

Sequence

>retro_amel_1892
AGTCTGCCAGGTGTGGAGACCCGGCACAAGAACATAGACATCTTAGTCATTCGGGAAAACACAGAGGGTGAATACAGCAA
CCTGGAGCACGAGAGTGTGAAAGGAGTGATTGAGAGCCTCAAAATCATTACCAAGGCCAAGTCTTTGTGCATTGCTGAAT
ATGCCTTTCAGCTGGCCCAAGTGATGAGGCTCAGGAAAGTGACAGCTGTACATAAGGCCAACATCGTGAAACTAGGAGAT
GGTCTCTTCCTCCAGTGTTGCAGGGAAGTGGCCTCCCACTATCCTCAGCTCACCTTTGAGGGCATGATTGTGGATAACAC
CACCATGCAGCTGGTATCCCGGCCCTAGCAGTTTGATGTGATGGTGATGCCCAATCTTTATGGAAACATCATCAACAATG
TCTGTGCAGGGTTGGTTGGGGGAGCGGGCCTTGTGCCTGGTGCAAACTATGGCCCTGCATATGCAGTGTTTGAAACAGCT
TCAAGGCAGTCAGGCAGAAATTTAGCCAATAAGAATATGGCCAACCCTATTGCCATGCTGCTGGCAAGCTGTATTATGCT
GGATTACCTCAAGCTCCACTCCTATGCCACCTGCATTCGCACTGCAGTCTTGGCATCCATTGAGAACAAAGATGTCCATA
CTCCAGACATTGGAGGCCAGAGTACCACACTGGATATCGTTCAAAATATAATAAGCCACATCAGTACTGTCAAT

Alignment

ORF - retro_amel_1892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.89 %
• Parental protein coverage: 60.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLPGVVTRHRDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQESGRKKVTAV
          SLPGV.TRH..IDIL..RENTEGEYS.LEHESV.GV.ESLKIITKAKSL.IAEYAF.LAQ.....KVTAV
Retrocopy SLPGVETRHKNIDILVIRENTEGEYSNLEHESVKGVIESLKIITKAKSLCIAEYAFQLAQVMRLRKVTAV

Parental  HKANIMKLGDGLFLQCCKEVAARYPQITFESMIVDNTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLVG
          HKANI.KLGDGLFLQCC.EVA..YPQ.TFE.MIVDNTTMQLVSRP.QFDVMVMPNLYGNI.NNVCAGLVG
Retrocopy HKANIVKLGDGLFLQCCREVASHYPQLTFEGMIVDNTTMQLVSRP*QFDVMVMPNLYGNIINNVCAGLVG

Parental  GPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRKAVLASMDNE
          G.GLV.GANYG..YAVFETA.R..G...ANKN.ANP.A.LLASC.MLD.LKLHSYAT.IR.AVLAS..N.
Retrocopy GAGLVPGANYGPAYAVFETASRQSGRNLANKNMANPIAMLLASCIMLDYLKLHSYATCIRTAVLASIENK

Parental  NMHTPDIGGQGTTSEAIQDIIRHIRIIN
          ..HTPDIGGQ.TT....Q.II.HI...N
Retrocopy DVHTPDIGGQSTTLDIVQNIISHISTVN

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_1892 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1892 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 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018466	1 retrocopy	retro_amel_1892 ,
Bos taurus	ENSBTAG00000001059	1 retrocopy	retro_btau_1194,
Canis familiaris	ENSCAFG00000019286	1 retrocopy	retro_cfam_1023,
Callithrix jacchus	ENSCJAG00000011185	1 retrocopy	retro_cjac_1597,
Equus caballus	ENSECAG00000018509	1 retrocopy	retro_ecab_941,
Homo sapiens	ENSG00000067829	1 retrocopy	retro_hsap_759,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Loxodonta africana	ENSLAFG00000006904	1 retrocopy	retro_lafr_560,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Mustela putorius furo	ENSMPUG00000008781	1 retrocopy	retro_mputfur_644,
Mus musculus	ENSMUSG00000002010	1 retrocopy	retro_mmus_134,
Nomascus leucogenys	ENSNLEG00000013540	1 retrocopy	retro_nleu_394,
Otolemur garnettii	ENSOGAG00000006735	1 retrocopy	retro_ogar_25,
Pteropus vampyrus	ENSPVAG00000013163	1 retrocopy	retro_pvam_373,
Rattus norvegicus	ENSRNOG00000037284	1 retrocopy	retro_rnor_209,
Sus scrofa	ENSSSCG00000012783	1 retrocopy	retro_sscr_662,
Tursiops truncatus	ENSTTRG00000011728	1 retrocopy	retro_ttru_848,