RetrogeneDB ID: retro_amel_1120

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192920.1:284531..285179(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC6
• Ensembl ID: ENSAMEG00000015401
• Aliases: None
• Description: zinc finger, DHHC-type containing 6 [Source:HGNC Symbol;Acc:19160]

Sequence

>retro_amel_1120
CAGGATAGTAAAGTCTGCCAAGCATACAAGGCACCACGGTCGCGTCACTGCAGAAGGTCTAACAGATGTGCGAGGAAAGA
GACCATCACTGTCCTTGGAGCAACAGTTGTCGTGGTTCACAAAATCACACTTCCTTCACACTGTTTCTCCTTTGAGCACC
ACCAGCTTGTATTCATGCTGCCTTCATCTTTGTTATGACTATGTTGACACAGCTTTATAGTTGGCTCTTCTTCAGGTGAA
ACATGGTGAAGATCGATATGCATGCAGCTTGGAGAGATCCTTTTCCAATCAGTCCCTTTGAGTTAGCAGCACTTGCAGCC
ACCTTGTTTGCCTTGGGATTAGCTTTAGGAACAACTGTAACTGTTGGGATGTTATTTTGTAACCAGATGAAAACAATTTG
CACAAACAAAACTTCTATTGAACCATGGATTGAAGAAAAGGCTAAAGATCGATTTCAATATTACCAACTAGATGAGGTCT
TTGTCTTAACTTATGATATGGGAAGTAGATGGAAGACTTTAAACAGGTATTTACATGGTCAGGGCCCCTAAAGGAGATGG
GCTAGAGCGGCCAATTAGAGAAGGTTGTCACCAGTAGAACTTAATAGTAGAACAATTGAAACAAAAAACAGATAAAAGAG
TCAGAAGT

Alignment

ORF - retro_amel_1120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.91 %
• Parental protein coverage: 52.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QYCKVCQAYKAPRSHHCRKCNRCVMK-MDHHCPWINNCCGYQNHASFTLFLLLAPLGCIHAAFIFVMTMY
          Q..KVCQAYKAPRS.HCR..NRC..K..DHHCPW.N.C.G.QNH.SFTLFLL.AP..CIHAAFIFVMTM.
Retrocopy QDSKVCQAYKAPRSRHCRRSNRCARK<RDHHCPWSNSCRGSQNHTSFTLFLL*APPACIHAAFIFVMTML

Parental  TQLYNRLSFGWNTVKIDMSAARRDPLPIIPFGLAAFAATLFALGLALGTTIAVGMLFFIQMKIILRNKTS
          TQLY..L.F..N.VKIDM.AA.RDP.PI.PF.LAA.AATLFALGLALGTT..VGMLF..QMK.I..NKTS
Retrocopy TQLYSWLFFR*NMVKIDMHAAWRDPFPISPFELAALAATLFALGLALGTTVTVGMLFCNQMKTICTNKTS

Parental  IESWIEEKAKDRIQYYQLDEVFVFPYDMGSRWK-NFKQVFTWSG-VPKGDGLAWPIREGCHQYSLTIEQL
          IE.WIEEKAKDR.QYYQLDEVFV..YDMGSRWK..FKQVFTWSG..PKGDGL..PIREGCHQ..L..EQL
Retrocopy IEPWIEEKAKDRFQYYQLDEVFVLTYDMGSRWK<DFKQVFTWSG<APKGDGLERPIREGCHQ*NLIVEQL

Parental  KQKADKRIRS
          KQK.DKR.RS
Retrocopy KQKTDKRVRS

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_1120 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1120 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015401	1 retrocopy	retro_amel_1120 ,
Canis familiaris	ENSCAFG00000010960	1 retrocopy	retro_cfam_2178,
Choloepus hoffmanni	ENSCHOG00000012828	1 retrocopy	retro_chof_1480,
Felis catus	ENSFCAG00000030784	1 retrocopy	retro_fcat_1193,
Loxodonta africana	ENSLAFG00000008129	1 retrocopy	retro_lafr_304,
Mustela putorius furo	ENSMPUG00000002043	1 retrocopy	retro_mputfur_668,
Mus musculus	ENSMUSG00000024982	1 retrocopy	retro_mmus_1740,
Otolemur garnettii	ENSOGAG00000030535	1 retrocopy	retro_ogar_1652,
Ictidomys tridecemlineatus	ENSSTOG00000013840	1 retrocopy	retro_itri_308,
Tarsius syrichta	ENSTSYG00000009673	2 retrocopies	retro_tsyr_1653, retro_tsyr_1771,