RetrogeneDB ID: retro_amel_1196

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193028.1:674140..674494(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMG4
• Ensembl ID: ENSAMEG00000014430
• Aliases: None
• Description: proteasome (prosome, macropain) assembly chaperone 4 [Source:HGNC Symbol;Acc:21108]

Sequence

>retro_amel_1196
GCCGCCGCGGGCAGGGATGTCTTTCTACACAACTTCCTCAGGAGGCTGGGGGAGCAGCTTGTCCACTTCCATGTCATGCA
GCTGATGGACTTGCTCTTCCTGTGGGTGGGGGCCATGCCACACCTGCACAAAATCGCAGTGGCCATGTGCAACTGCTACG
ATTCCATCCCGGTGTCTACTTCCCTCCTCGGAGACACTTCTGACACAATCTCCGCTGGCCTTGCCTGGCGCTTAGCCAGG
AAGACGGACAAACAGGTATTTGTCAGCTATAACCTTCAAAACACAGACAGTAACTTCCCATTACTGGTAGAAAACAGGAT
CAAGGAAGAAATGGAGGCTTTTCTGGAAAAGTTC

Alignment

ORF - retro_amel_1196 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.9 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAGGGDVSLHNFSARLWEQLVHFHVMRLTDSLFLWVGATPHLRNLAVAMCNRYDSIPVSTSLLGDTSDTT
          AA.G.DV.LHNF..RL.EQLVHFHVM.L.D.LFLWVGA.PHL...AVAMCN.YDSIPVSTSLLGDTSDT.
Retrocopy AAAGRDVFLHNFLRRLGEQLVHFHVMQLMDLLFLWVGAMPHLHKIAVAMCNCYDSIPVSTSLLGDTSDTI

Parental  STGLAQRLARKTNKQVFVSYNLQNTDSNFPLLVENRIKEEMEAFPEKF
          S.GLA.RLARKT.KQVFVSYNLQNTDSNFPLLVENRIKEEMEAF.EKF
Retrocopy SAGLAWRLARKTDKQVFVSYNLQNTDSNFPLLVENRIKEEMEAFLEKF

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_1196 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1196 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014430	1 retrocopy	retro_amel_1196 ,
Bos taurus	ENSBTAG00000031249	1 retrocopy	retro_btau_1040,
Myotis lucifugus	ENSMLUG00000024906	1 retrocopy	retro_mluc_802,
Rattus norvegicus	ENSRNOG00000039265	2 retrocopies	retro_rnor_1442, retro_rnor_766,
Sus scrofa	ENSSSCG00000001005	3 retrocopies	retro_sscr_362, retro_sscr_656, retro_sscr_657,
Tursiops truncatus	ENSTTRG00000006146	2 retrocopies	retro_ttru_1531, retro_ttru_1849,