RetrogeneDB ID: retro_amel_105

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193713.1:397977..398841(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000018812
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM122B
• Ensembl ID: ENSAMEG00000001311
• Aliases: None
• Description: family with sequence similarity 122B [Source:HGNC Symbol;Acc:30490]

Sequence

>retro_amel_105
ATGGCTCAGGAGAAGATGGAGCTAGACCTGGAGTTGCCTCCGGGTACTGGCGGGAGCCCGACGGAGGGAGGCGGCAGTGG
CGCCGGCGGGGGCCTCAGGAGGTCTAACAGCGCCCCCCTGATCCACGGCCTCAGTGACACTTCGCCGGTGTTCCAGGCCG
AGGCGCCAAGCGCCAGGCGGAACAGCACAACGTTCCCGAACCGCCACGGCCTGCTGCTGCCAGCCTCACCCGTCCGCATG
CACAGCAGCCGCTTGCACCAGATCAAACAGGAGGAGGGCATGGACTTGATCAACCGAGAGACCGTCCACGAGCGCGAGGT
GCAGAACGCAATGCAGATAAGCCACTCCTGGGAGGAAAGTTTCAGCCTGAGTGACAACGACGTGGAGAAGTCCGCCTCCC
CGAAGCGCATCGATTTCATTCCGGTGTCACCAGCACCGTCACCCACCCGGGGGATTGGGAAGCAGTGTTTTTCACCATCC
TTGCAAAGTTTTGTGAGTAGCAATGGATTGCCTCCAAGTCCTATTCCCAGCCCAACGACTCGATTTACTACCCGGAGAAG
CCAGAGTCCCATCAATTGCATTAGACCAAGTGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGAATATCAGC
CAAAGAGATTTTTCCAGGGCATCACCAACATGCTTTCTTCTGACGTTGCACAGCTGTCAGATCCTGGTGTGTGTGTATCG
TCTGATACCCTTGACGGAAACAGCAGCAGTGCCGGATCTTCTTGTAACTCACCAGCGAAAGTCAGCACTACCACCGACTC
TCCTGTGTCGCCTGCCCAAGCGGCTTCTCCATTTATTCCAGTAGATGAACTTTCATCGAAGTGA

Alignment

ORF - retro_amel_105 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 92.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGTLRRSSSAPLIHGLSDLSQVFQPYTFRTRRNSTTIMSRHSLLLSSSPNRVPSSRLHQIKREEGMDMMN
          GG.LRRS.SAPLIHGLSD.S.VFQ......RRNSTT...RH.LLL..SP.R..SSRLHQIK.EEGMD..N
Retrocopy GGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPNRHGLLLPASPVRMHSSRLHQIKQEEGMDLIN

Parental  RETAHEREVQTAMQISQSWDESLSLSDSDFEKPEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQMFV
          RET.HEREVQ.AMQIS.SW.ES.SLSD.D.EK.....SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.FV
Retrocopy RETVHEREVQNAMQISHSWEESFSLSDNDVEKSA---SPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFV

Parental  SSSGLPPSPVPSP-RRFMRRRSQSPVKCIRPSVLGPLKRKGEMETESQPKRLFQGTTSMLSPEAAQLSDL
          SS.GLPPSP.PSP..RF..RRSQSP..CIRPSVLGPLKRK.EMETE.QPKR.FQG.T.MLS...AQLSD.
Retrocopy SSNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSDP

Parental  SSCFVLSSDILDGSSSSSGLSSDSLAKGSTTAESPVACSNSCSPFILMDDLSPK
          ..C...SSD.LDG.SSS.G.S..S.AK.STT..SPV......SPFI..D.LS.K
Retrocopy GVC--VSSDTLDGNSSSAGSSCNSPAKVSTTTDSPVSPAQAASPFIPVDELSSK

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_105 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_105 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 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001311	1 retrocopy	retro_amel_105 ,
Bos taurus	ENSBTAG00000001886	1 retrocopy	retro_btau_103,
Canis familiaris	ENSCAFG00000018882	1 retrocopy	retro_cfam_181,
Callithrix jacchus	ENSCJAG00000004313	1 retrocopy	retro_cjac_594,
Cavia porcellus	ENSCPOG00000011218	1 retrocopy	retro_cpor_80,
Equus caballus	ENSECAG00000018643	1 retrocopy	retro_ecab_91,
Felis catus	ENSFCAG00000024842	1 retrocopy	retro_fcat_1575,
Myotis lucifugus	ENSMLUG00000007988	1 retrocopy	retro_mluc_382,
Macaca mulatta	ENSMMUG00000016948	1 retrocopy	retro_mmul_185,
Mustela putorius furo	ENSMPUG00000012690	1 retrocopy	retro_mputfur_64,
Mus musculus	ENSMUSG00000036022	1 retrocopy	retro_mmus_22,
Rattus norvegicus	ENSRNOG00000050146	1 retrocopy	retro_rnor_651,
Sus scrofa	ENSSSCG00000012685	1 retrocopy	retro_sscr_60,
Ictidomys tridecemlineatus	ENSSTOG00000006261	1 retrocopy	retro_itri_61,