RetrogeneDB ID: retro_amel_1909

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195682.1:4164..4458(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPV
• Ensembl ID: ENSAMEG00000004716
• Aliases: None
• Description: centromere protein V [Source:HGNC Symbol;Acc:29920]

Sequence

>retro_amel_1909
AAGAAGCAGCACCGACACTTCCTCGTCCCGGCCTCGCGCTTCACTCTCCTGCTGGGCGCCGAGAGCATCGTCACCTATCG
ATCCCACACGCACCCCGCGCTGCACAGCTTCTGCAGCAGGTGCGGGGTGCAGAGTTTCCACGCCTCTGTCTCTGACCCCG
GCGTGTATGGCGTCGCCCCGCACTGCCTGGACGCCGGCACCGTGCGCAGTGTGGTCATCGAAGAGGTCGACGGTGGCGAC
TGGGGGGAGGAGGCCGTGGAGGAGCCCAAGGCCATCCAGAGCGCGTCCCCCGAG

Alignment

ORF - retro_amel_1909 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.31 %
• Parental protein coverage: 64.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKQNRHFIVPASRFKLLKGAESITTYTFNTHKAQHTFCKRCGVQSFYTPRSNPGGFGIAPHCLDEGTVRS
          KKQ.RHF.VPASRF.LL.GAESI.TY...TH.A.H.FC.RCGVQSF....S.PG..G.APHCLD.GTVRS
Retrocopy KKQHRHFLVPASRFTLLLGAESIVTYRSHTHPALHSFCSRCGVQSFHASVSDPGVYGVAPHCLDAGTVRS

Parental  VVIEEFNGTDW-EKAMKEHKTIKNMSKE
          VVIEE..G.DW.E.A..E.K.I...S.E
Retrocopy VVIEEVDGGDWGEEAVEEPKAIQSASPE

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_1909 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1909 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004716	5 retrocopies	retro_amel_1859, retro_amel_1870, retro_amel_1909 , retro_amel_1926, retro_amel_924,
Canis familiaris	ENSCAFG00000018019	2 retrocopies	retro_cfam_2153, retro_cfam_2155,
Homo sapiens	ENSG00000166582	3 retrocopies	retro_hsap_4683, retro_hsap_4833, retro_hsap_4834,
Macropus eugenii	ENSMEUG00000002027	1 retrocopy	retro_meug_519,
Microcebus murinus	ENSMICG00000007166	1 retrocopy	retro_mmur_1491,
Mustela putorius furo	ENSMPUG00000010146	2 retrocopies	retro_mputfur_1195, retro_mputfur_39,
Nomascus leucogenys	ENSNLEG00000014726	1 retrocopy	retro_nleu_2709,
Otolemur garnettii	ENSOGAG00000029365	1 retrocopy	retro_ogar_99,
Pan troglodytes	ENSPTRG00000008810	1 retrocopy	retro_ptro_3216,
Ictidomys tridecemlineatus	ENSSTOG00000012221	2 retrocopies	retro_itri_110, retro_itri_1540,