RetrogeneDB ID: retro_amel_1870

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195016.1:58438..58794(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000016949
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_amel_1870
CTCAGCTGCGAGGGTGCCGCCAAGTTCCTGCTGCACACCTTCGAATACCCAGGCCTGGTGTATCACACGGGAGGCTGCCA
CTGCGGCGCGGTCCGCTTCGCCGTCTGGGCCCCCGCAGACCTGCGCGTGGTGGATTGCAGCTGCAGGCTGTGCAGGAAGA
AGCAGCACCGACACTTCCTCCTCCCGGCCTCGCGCTTCACTCTCCTGCTGGGCGCCGAGAGCATCGTCACCTATCGATCC
CACACGCACCCCGCGCTGCACAGCTTCTGCAGCAGGTGCGGGGTGCAGAGTTTCCACGCCTCTGTCTCTGACCCGGCGAG
TATGGCGTCGCCCCGCACTGCCTGGACAAGGGAACA

Alignment

ORF - retro_amel_1870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.33 %
• Parental protein coverage: 78.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTFEGAAKLLLDTFEYQGLVRHTGGCHCGAVRFEVWASADLHIFDCNCSICKKKQNRHFIVPASRFKLLK
          L..EGAAK.LL.TFEY.GLV.HTGGCHCGAVRF.VWA.ADL...DC.C..C.KKQ.RHF..PASRF.LL.
Retrocopy LSCEGAAKFLLHTFEYPGLVYHTGGCHCGAVRFAVWAPADLRVVDCSCRLCRKKQHRHFLLPASRFTLLL

Parental  GAESITTYTFNTHKAQHTFCKRCGVQSFYTPRSN-PGGFGIAPHCLDEGT
          GAESI.TY...TH.A.H.FC.RCGVQSF....S..PG..G.APHCLD.GT
Retrocopy GAESIVTYRSHTHPALHSFCSRCGVQSFHASVSD<PGEYGVAPHCLDKGT

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_1870 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1870 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,