RetrogeneDB ID: retro_amel_617

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192530.1:1392652..1393076(+)
• Located in intron of: ENSAMEG00000008150

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB22A
• Ensembl ID: ENSAMEG00000012646
• Aliases: None
• Description: RAB22A, member RAS oncogene family [Source:HGNC Symbol;Acc:9764]

Sequence

>retro_amel_617
CTGCTACAGATTTCATTTGTAGGTAAATCAAGTATTGTATGGTAGTTTGTAGAGAATAGTTTTGAGCCTAAGATCATTTC
AGTAAGAGGGCATCTTTTGTCTAGAACCAAAATGAGCATGTAAATTTCTTAATCTGGGATATAGCTGCACAACAATGATT
TTCTGCTTTACCAGAATGTACTATTATAGTTGTCTTTAGCTATAATGATTTATGATACCAAAAAGGAAATATTTTCAACA
TTAAGGAATCAATTAAGAGATTGACAGCAAGACCCATCTAATTTTGTAGTTGACATTGCAAGAAATAAGTGTGATATTAT
CATAAAAGGGAAGTCATGGAGAGAGATGCTAAGGACTCCACTGACTCATCCGTACAGTTTTTGTAGAGATCAGTGCAAAA
ACCACAATGAACTTAAATGAACTC

Alignment

ORF - retro_amel_617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.25 %
• Parental protein coverage: 79.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LFQDTGVGKSSIVWRFVEDSFDPNINPTIG-ASFMTKTVQYQNELHKFLIWDTAGQERFRAL-APMYYRG
          L.Q...VGKSSIVW.FVE.SF.P.I....G.ASF........N....FLIWD.A.Q..F.AL...MYY..
Retrocopy LLQISFVGKSSIVW*FVENSFEPKIISVRG<ASFV*NQNEHVN----FLIWDIAAQQ*FSAL<TRMYYYS

Parental  S-AAAIIVYDITKEETFSTLKNWVKELRQHGPPNIVVAIAGNKCDLI-DVREVMERDAKDYADS-IHAIF
          ....AI..YD.TK.E.FSTL.N......Q..P.N.VV.IA.NKCD.I...REVMERDAKD..DS.I...F
Retrocopy C<SLAIMIYD-TKKEIFSTLRNQLRD*QQ-DPSNFVVDIARNKCDII<HKREVMERDAKDSTDS<IRTVF

Parental  VETSAKNAININEL
          VE.SAK...N.NEL
Retrocopy VEISAKTTMNLNEL

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_617 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_617 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Ailuropoda melanoleuca	ENSAMEG00000006003	1 retrocopy	retro_amel_543,
Ailuropoda melanoleuca	ENSAMEG00000012646	1 retrocopy	retro_amel_617 ,
Canis familiaris	ENSCAFG00000012101	1 retrocopy	retro_cfam_501,
Callithrix jacchus	ENSCJAG00000019039	2 retrocopies	retro_cjac_1715, retro_cjac_842,
Microcebus murinus	ENSMICG00000008382	1 retrocopy	retro_mmur_1546,
Oryctolagus cuniculus	ENSOCUG00000004414	1 retrocopy	retro_ocun_554,
Otolemur garnettii	ENSOGAG00000015779	1 retrocopy	retro_ogar_2851,