RetrogeneDB ID: retro_amel_1387

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193307.1:262784..263641(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000006872
• Aliases: None
• Description: None

Sequence

>retro_amel_1387
GAATGCTTCTCCATCCACATTGGTCAGGCTGGTGTCTAAATTGGCAATACCTGCTGGGAGCTTTATTGCCTGGAACACGG
CATCCAGCATGATGGTCAGGTGCCAAGTGACAAAACCACCAGAGGAGGAGACGATCCCTTCACACTTTCTCCAGTGAGAA
GAGGTGTTGGCAGGCATGTGCCCAGGGCCATGTTTGTAGACCTGGAACCCACAGTCATTGATGAAGTTCACCCTGGCACC
TACTGAGAGTTCTTCCACCCTGAGAAGCTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGCCTGCAAGCCTGACTT
CATTAGCAAGGAGATCGTTGACCCTGTTTTGGACTGTATTCCAAAACTGGCTGACCAGGGCACAGGTCTTCAGGGGTTCT
TGGTTTTCCACAGCTTTGGAGAGGGACTGGTTCTGGGTTCATCTCCCTGCTGATGGAACAACTGTCTGTTGATTATGGCA
AGAAGTCCAAGCTGGACTTCTCCATTTAGCCAGCCCCCCGGGTATCCACAGCTCTAGTTGAGCTCGACAGCTCCATCCTC
ACTACGGACACCCTGGAGCACTATGATTTTTCCTCTGTGGTAGACGATTATGCCATCTGTGACATCTGTCATAGAAACCT
CAATATTGAACTCCCAACATACACTAACCTGAATAGGTTGATAGGTCAAATTATGTCCTCCATCACTGCTTCCCTCAGAT
TTGATGGAGCCCTGAATATTGATCTGACAGAATTTCAGACCAAGCTAGTACCCTATCCCTGCTTCTATTTCCCTCTGGCC
ACATATGTCCCTGTCATCTCTGCTGAGAAATCTTACTATGAACAGCTTTCTATAGCA

Alignment

ORF - retro_amel_1387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.69 %
• Parental protein coverage: 63.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEP
          EC.SIH.GQAGV.IGN.CWELYCLEHGIQ.DGQ.PSDKT..GGDD.F.......G.G.HVPRA.FVDLEP
Retrocopy ECFSIHIGQAGV*IGNTCWELYCLEHGIQHDGQVPSDKTTRGGDDPFTLSPVRRGVGRHVPRAMFVDLEP

Parental  TVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFG
          TVIDEV..GTY...FHPE.LITGKEDAANNYA.....I.KEI.D.VLD.I.KLADQ.TGLQGFLVFHSFG
Retrocopy TVIDEVHPGTY*EFFHPEKLITGKEDAANNYACKPDFISKEIVDPVLDCIPKLADQGTGLQGFLVFHSFG

Parental  -GGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
          ..GTGSGF.SLLME.LSVDYGKKSKL.FSI.PAP.VSTA.VE...SILTT..TLEH.D....VD..AI.D
Retrocopy <RGTGSGFISLLMEQLSVDYGKKSKLDFSI*PAPRVSTALVELDSSILTT-DTLEHYDFSSVVDDYAICD

Parental  ICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPCIHFPLATYAPVISAEKA
          IC.RNL.IE.PTYTNLNRLI.QI.SSITASLRFDGALN.DLTEFQT.LVPYPC..FPLATY.PVISAEK.
Retrocopy ICHRNLNIELPTYTNLNRLIGQIMSSITASLRFDGALNIDLTEFQTKLVPYPCFYFPLATYVPVISAEKS

Parental  YHEQLSVA
          Y.EQLS.A
Retrocopy YYEQLSIA

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_1387 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1387 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 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006872	4 retrocopies	retro_amel_1162, retro_amel_1367, retro_amel_1387 , retro_amel_1895,
Ailuropoda melanoleuca	ENSAMEG00000011042	2 retrocopies	retro_amel_488, retro_amel_518,
Canis familiaris	ENSCAFG00000008640	8 retrocopies	retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463, retro_cfam_926,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Cavia porcellus	ENSCPOG00000013016	1 retrocopy	retro_cpor_96,
Felis catus	ENSFCAG00000027011	1 retrocopy	retro_fcat_588,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Loxodonta africana	ENSLAFG00000010021	1 retrocopy	retro_lafr_326,
Microcebus murinus	ENSMICG00000017551	3 retrocopies	retro_mmur_144, retro_mmur_705, retro_mmur_885,
Myotis lucifugus	ENSMLUG00000002622	4 retrocopies	retro_mluc_154, retro_mluc_186, retro_mluc_234, retro_mluc_270,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Tupaia belangeri	ENSTBEG00000001671	1 retrocopy	retro_tbel_3700,
Tarsius syrichta	ENSTSYG00000013266	7 retrocopies	retro_tsyr_1014, retro_tsyr_1278, retro_tsyr_1281, retro_tsyr_1679, retro_tsyr_1834, retro_tsyr_243, retro_tsyr_6,
Tursiops truncatus	ENSTTRG00000004794	1 retrocopy	retro_ttru_407,