RetrogeneDB ID: retro_amel_383

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192415.1:813297..813730(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSAMEG00000006082
• Aliases: None
• Description: ras homolog family member Q [Source:HGNC Symbol;Acc:17736]

Sequence

>retro_amel_383
CCCACCATCTTCAGTGCAGTCCTCATCCATGTAGAGAGCAGGCAGTACCTTCTGAGGCTCTGTGACACGAGTATGACCAG
ACAGGAAAACTGTGATCCTCTGAGGCCTTTCTCTTATCCAGTGACTGTTGTCTTCCTTATATGCTGCCCTCTGAACTCAT
TTCATAATGCGAAGGAAGAGTGGGCACCAGAACTTAAGGAATACACACTAAATGTGCCTCATTTAATAGGAACTCAGAGT
CTGATCTGCAAGGTGACCCCAAAGCTTTGGCAAGACTGAATAACATGAAAGAAAAACCTGTATGTGTAAAAGAAGGATAG
AAACTAGCAAAAGAGATGGGAGCTCCCATGTGGAAAGTTCAGCTTTAACCCAGAAAGGATTGAAGGCAGTGTGTGATGAG
GCTGTCATAGCCATTTTAACTCCAAAGAAACAC

Alignment

ORF - retro_amel_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.26 %
• Parental protein coverage: 88.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PTSALAVSVTVGGKQYLLGLYDTA--GQEDYDRLRPLSYPMTDVFLICFSVVNPA-SFQNVKEEWVPELK
          PT...AV...V...QYLL.L.DT....QE..D.LR....P........F....P..SF.N.KEEW.PELK
Retrocopy PTIFSAVLIHVESRQYLLRLCDTSMTRQENCDPLR----PFSYPVTVVFLICCPLNSFHNAKEEWAPELK

Parental  EYAPNVPFLL-IGTQIDLRDDPKTLARLNDMKEKPICVEQGQKLA-KEIGACCYVECSALTQKGLKTVFD
          EY..NVP.L.......DL..DPK.LARLN.MKEKP.CV..G.KLA.K..G....VE.SALTQKGLK.V.D
Retrocopy EYTLNVPHLI<RNSESDLQGDPKALARLNNMKEKPVCVKEG*KLA<KRDGSS-HVESSALTQKGLKAVCD

Parental  EAIIAILTPKKH
          EA.IAILTPKKH
Retrocopy EAVIAILTPKKH

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_383 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_383 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006082	1 retrocopy	retro_amel_383 ,
Ailuropoda melanoleuca	ENSAMEG00000009889	2 retrocopies	retro_amel_1691, retro_amel_647,
Ailuropoda melanoleuca	ENSAMEG00000017364	1 retrocopy	retro_amel_1104,
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
Echinops telfairi	ENSETEG00000019234	3 retrocopies	retro_etel_1468, retro_etel_596, retro_etel_672,
Felis catus	ENSFCAG00000015608	1 retrocopy	retro_fcat_795,
Myotis lucifugus	ENSMLUG00000001567	1 retrocopy	retro_mluc_595,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tursiops truncatus	ENSTTRG00000011892	1 retrocopy	retro_ttru_805,