RetrogeneDB ID: retro_amel_930

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192753.1:1107496..1107915(+)
• Located in intron of: ENSAMEG00000017009

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENOPH1
• Ensembl ID: ENSAMEG00000005140
• Aliases: None
• Description: enolase-phosphatase 1 [Source:HGNC Symbol;Acc:24599]

Sequence

>retro_amel_930
AAAGAAGAGGAGTGCCAGCAGGACCTCAGTCCTTTGCGGTAACAGGCCGAAGAGGATTCCCATCGGGATAGGGTATTTTG
ACCTCTGCAACATCTGGGAATGGGGTGGATGATCTGCAAGAGATGATCCAGGCTGCGGTAGATAATGTGTGCTGGCAGAG
ATCTCTGGGTGCAAAGACCATGGCACTGACAGAAATGCAAGGCTTCTGTGGAAGGCAGCCTTTTACAGCTGGGAGAGTAA
GAGCGGCATTCACTGAATATGTCGTTCCAGCAGCTAGGAAGTGGAGAGAGGCTGGAACGAGGGTGTCTCTCTATTCCTCG
GGGAGGGTAGGGGCACAGAAACTATGACGTGTGCATTCTACAGAGGAAGGTGTTCTTGAGCTTGTGGTTAGTTTCTTTGA
TGCCAAGGTTGGGCATAAG

Alignment

ORF - retro_amel_930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.99 %
• Parental protein coverage: 53.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEEECQQDVSLLRKQAEEDSHLDGA-VPIPAASGHGGGDPQQMIQAVVDNVCWQMSLDRKTTALKQLQGH
          .EEECQQD.S.LR.QAEEDSH.D.......A.SG.G..D.Q.MIQA.VDNVCWQ.SL..KT.AL...QG.
Retrocopy KEEECQQDLSPLR*QAEEDSHRDRV<ILTSATSGNGVDDLQEMIQAAVDNVCWQRSLGAKTMALTEMQGF

Parental  MWRAAFAAGRMKAEFFEDVVPAVRKWREAGMKVYIYSSGSVEAQKLLFGHSTEGDILELVDGHFDTKIGH
          ..R..F.AGR..A.F.E.VVPA.RKWREAG..V..YSSG.V.AQKL...HSTE...LELV...FD.K.GH
Retrocopy CGRQPFTAGRVRAAFTEYVVPAARKWREAGTRVSLYSSGRVGAQKL*RVHSTEEGVLELVVSFFDAKVGH

Parental  K
          K
Retrocopy K

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_930 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_930 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005140	2 retrocopies	retro_amel_1186, retro_amel_930 ,
Choloepus hoffmanni	ENSCHOG00000003283	4 retrocopies	retro_chof_2150, retro_chof_470, retro_chof_486, retro_chof_596,
Callithrix jacchus	ENSCJAG00000015251	2 retrocopies	retro_cjac_1376, retro_cjac_2375,
Equus caballus	ENSECAG00000019612	1 retrocopy	retro_ecab_164,
Erinaceus europaeus	ENSEEUG00000004274	1 retrocopy	retro_eeur_563,
Homo sapiens	ENSG00000145293	1 retrocopy	retro_hsap_2900,
Gorilla gorilla	ENSGGOG00000003719	1 retrocopy	retro_ggor_2010,
Loxodonta africana	ENSLAFG00000008619	1 retrocopy	retro_lafr_1158,
Macropus eugenii	ENSMEUG00000011458	1 retrocopy	retro_meug_1125,
Myotis lucifugus	ENSMLUG00000014460	1 retrocopy	retro_mluc_2504,
Otolemur garnettii	ENSOGAG00000002502	1 retrocopy	retro_ogar_1549,
Pongo abelii	ENSPPYG00000014887	1 retrocopy	retro_pabe_2399,
Pan troglodytes	ENSPTRG00000016218	1 retrocopy	retro_ptro_1960,
Tursiops truncatus	ENSTTRG00000001800	1 retrocopy	retro_ttru_1231,