RetrogeneDB ID: retro_amel_204

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192352.1:3361327..3362384(-)
• Located in intron of: ENSAMEG00000002940

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA3
• Ensembl ID: ENSAMEG00000010117
• Aliases: None
• Description: ubiquitin-like modifier activating enzyme 3 [Source:HGNC Symbol;Acc:12470]

Sequence

>retro_amel_204
AAGAAGAAAAGAAGAATAGAGGAGCTGCTGACTGAGAAAGTGGCTGTTGGTGGTGTGTGTGGGGACACTGGAGACTGGGA
AGGTCGCTGGAACCATGTAAAGAAGTTCCTCAAGTGATCTGTACCTTTCACACATCCTGATTTTGAACCGAGCACTGAAT
CTCTCCAGTTTTTGTTAGATACATGTAAAGTTCTGGTCATTGGAGCTGGCAGCTTAGGATGTGAGCTCCTGAAAAATCTG
GCGTTGTCTGGTTTTAGACAGATTTATATTACAGACATGGACACTATAGATGTTTCCAGTCTAAAAAGCAGTTTTTATAT
AGGCCTAAAGATGTTGAAAGACCTAAGGCTGAAGTTGCTGCAGAATTTCTAAATGACAGAGCTTCTAATTGTAATGTAGT
TCCACATTTCAACAAGATTTCAGGATTTTAATGACACTTTCTATCAACAGTTTCATATAATTGTGTGTGGACTGGACCCT
ATCATAGCCAGAAGATGGATAAATGGCATGCTGATATCTCTTCTAAATTATGAAGATGGTGTATTAGATCCAAGCTCCAT
TGTCCCTTTGATAGATGGGGGGACAGAAGGTTTTAAAGGAAATGCCATGGTGATTCTGCCTGGAATGACTGCTTGTATTG
AATGCACCCTAGTACTGTATCCTCCACAGGTTAATTTTCCCATGTGCACCATTGCGTCTATGTCCAGGCTACTAGAACAC
TGCATTGAGTAGTAAGGATACTGCAGCGGCCTAAGGAGCAGCTTTTGGAGAAGGAGTTCTATTAGGGGGAGATGATCCTG
ATCATATTCAGTGGATTTTCCAAAAGTCCGTCGAGAGAGAATCGCAGTATAATATTAGGGGTGTTACCTGTAGACTCACT
CAAGGAGTAGTAAAACGAATCATTCCTGCAGTAGCTTCTACAAATACAGTCATTGCAGCTGTGTGTGCCACTGATGTTTT
TAAAATAGCCACAAGTGCATATATTCCTCTTAATACTTGGTATTCAGTGATGTAGATGGACTGTACACATACACATTTGA
AGCAGAGAGAAAGGAAA

Alignment

ORF - retro_amel_204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.31 %
• Parental protein coverage: 77.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKRRRIEELLAEKMAVDGGCGDTGDWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAG
          KK.RRIEELL.EK.AV.G.CGDTGDWEGRWNHVKKFL..S.PFTHPDFEPSTESLQFLLDTCKVLVIGAG
Retrocopy KKKRRIEELLTEKVAVGGVCGDTGDWEGRWNHVKKFLK*SVPFTHPDFEPSTESLQFLLDTCKVLVIGAG

Parental  GLGCELLKNLALSGFRQIHVIDMDTIDVSNL-NRQFLFRPKDVGRPKAEVAAEFLNDRVPNCNVVPHFNK
          .LGCELLKNLALSGFRQI...DMDTIDVS.L...QFL.RPKDV.RPKAEVAAEFLNDR..NCNVVPHFNK
Retrocopy SLGCELLKNLALSGFRQIYITDMDTIDVSSL<KKQFLYRPKDVERPKAEVAAEFLNDRASNCNVVPHFNK

Parental  I-QDFNDTFYRQFHIIVCGLDSVIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNAMVILPG
          I.QDFNDTFY.QFHIIVCGLD..IARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNAMVILPG
Retrocopy I>QDFNDTFYQQFHIIVCGLDPIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNAMVILPG

Parental  MTACIECTLELYPPQVNFPMCTIASMPRLPEHCIE-YVRILQWPKEQ-PFGEGIPLDGDDPDHIQWIFQK
          MTACIECTL.LYPPQVNFPMCTIASM.RL.EHCIE..VRILQ.PKEQ..FGEG..L.GDDPDHIQWIFQK
Retrocopy MTACIECTLVLYPPQVNFPMCTIASMSRLLEHCIE<VVRILQRPKEQ<AFGEGVLLGGDDPDHIQWIFQK

Parental  SLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTY
          S.ER.SQYNIRGVT.RLTQGVVKRIIPAVASTN.VIAAVCAT.VFKIATSAYIPLN........D...T.
Retrocopy SVERESQYNIRGVTCRLTQGVVKRIIPAVASTNTVIAAVCATDVFKIATSAYIPLNTWYSVM*MDCTHTH

Parental  TFEAERK
          ....ERK
Retrocopy LKQRERK

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_204 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_204 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010117	1 retrocopy	retro_amel_204 ,
Choloepus hoffmanni	ENSCHOG00000013626	2 retrocopies	retro_chof_1740, retro_chof_553,
Callithrix jacchus	ENSCJAG00000013395	2 retrocopies	retro_cjac_2827, retro_cjac_2986,
Erinaceus europaeus	ENSEEUG00000005430	2 retrocopies	retro_eeur_374, retro_eeur_663,
Otolemur garnettii	ENSOGAG00000007771	2 retrocopies	retro_ogar_1868, retro_ogar_2776,
Rattus norvegicus	ENSRNOG00000006221	1 retrocopy	retro_rnor_852,
Sus scrofa	ENSSSCG00000011506	1 retrocopy	retro_sscr_192,