RetrogeneDB ID: retro_amel_1920

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL196524.1:5806..6052(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSAMEG00000011031
• Aliases: None
• Description: None

Sequence

>retro_amel_1920
CAGAGAAAGTCTCCAGAGAATACGGAGGGCAAGGATGGATCCCAAGCAACTAAATAGGAGACCACCAGACTGTCTGCCAG
ATTGCCAGCGAAACCCACTCCACCAAAACCTGGACCTAAACCAAGAAAAACATCTGCTCACAAAGAACCCAGAAGAAAGA
CTCACACAGGGACTAAAAGGAAAGAGGGAGAGCACGACGCTGGAAAGGGCGGTCCTGTGCCATCTGAAAATGGTGAAACT
AAAGCT

Alignment

ORF - retro_amel_1920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.47 %
• Parental protein coverage: 63.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RNKSPENTDGKDGSKGTKQEPTRRSARLSAKPAPPKPEPKPRKTSAKKEPGTKVNKGVKGKKEEKQEAGK
          ..KSPENT.GKDGS..TK.E.TR.SARL.AKP.PPKP.PKPRKTSA.KEP..K...G.K..KE....AGK
Retrocopy QRKSPENTEGKDGSQATK*ETTRLSARLPAKPTPPKPGPKPRKTSAHKEPRRKTHTGTK-RKEGEHDAGK

Parental  EGTAPSENGETKA
          .G..PSENGETKA
Retrocopy GGPVPSENGETKA

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_1920 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1920 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011031	1 retrocopy	retro_amel_1920 ,
Bos taurus	ENSBTAG00000001422	2 retrocopies	retro_btau_1524, retro_btau_1558,
Canis familiaris	ENSCAFG00000002809	1 retrocopy	retro_cfam_1013,
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Callithrix jacchus	ENSCJAG00000010800	2 retrocopies	retro_cjac_1626, retro_cjac_819,
Mustela putorius furo	ENSMPUG00000018092	1 retrocopy	retro_mputfur_1164,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Pongo abelii	ENSPPYG00000016791	1 retrocopy	retro_pabe_421,