RetrogeneDB ID: retro_amel_1054

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192869.1:898493..898676(+)
• Located in intron of: ENSAMEG00000006583

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL2
• Ensembl ID: ENSAMEG00000005453
• Aliases: None
• Description: GABA(A) receptor-associated protein-like 2 [Source:HGNC Symbol;Acc:13291]

Sequence

>retro_amel_1054
CCTGCCACTGTCAGGAAGTGAATGTTCAAGGAGGACCACTTGCGGGAACACAGGTGCATGGAATCTGTGAAGATATGAGC
GAAATATCCTGACTGGGTTCTGGTGATTGTGAAAAAAGTTTCAGGCTCTCAGATTGTTGACAATGACAAATGGAAGTATC
TGGTTCCGTCTGACATCACTGTG

Alignment

ORF - retro_amel_1054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.05 %
• Parental protein coverage: 50.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAAAMKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITV
          PA...K.MFKEDH..EHRC.ES.KI.AKYPD.V.VIV.KVSGSQIVD.DK.KYLVPSDITV
Retrocopy PATVRK*MFKEDHLREHRCMESVKI*AKYPDWVLVIVKKVSGSQIVDNDKWKYLVPSDITV

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_1054 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1054 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 18 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005453	2 retrocopies	retro_amel_1054 , retro_amel_1238,
Ailuropoda melanoleuca	ENSAMEG00000018254	2 retrocopies	retro_amel_1660, retro_amel_873,
Canis familiaris	ENSCAFG00000031455	1 retrocopy	retro_cfam_639,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146,
Dasypus novemcinctus	ENSDNOG00000002240	2 retrocopies	retro_dnov_1755, retro_dnov_2332,
Erinaceus europaeus	ENSEEUG00000011134	1 retrocopy	retro_eeur_337,
Homo sapiens	ENSG00000034713	1 retrocopy	retro_hsap_4115,
Gorilla gorilla	ENSGGOG00000012299	2 retrocopies	retro_ggor_2761, retro_ggor_342,
Loxodonta africana	ENSLAFG00000017065	2 retrocopies	retro_lafr_234, retro_lafr_543,
Microcebus murinus	ENSMICG00000011981	1 retrocopy	retro_mmur_1473,
Myotis lucifugus	ENSMLUG00000015112	1 retrocopy	retro_mluc_1207,
Macaca mulatta	ENSMMUG00000005759	2 retrocopies	retro_mmul_2369, retro_mmul_540,
Mustela putorius furo	ENSMPUG00000009894	1 retrocopy	retro_mputfur_993,
Mus musculus	ENSMUSG00000031950	5 retrocopies	retro_mmus_2637, retro_mmus_2655, retro_mmus_3240, retro_mmus_456, retro_mmus_506,
Nomascus leucogenys	ENSNLEG00000013048	2 retrocopies	retro_nleu_1560, retro_nleu_580,
Pongo abelii	ENSPPYG00000007565	2 retrocopies	retro_pabe_3368, retro_pabe_372,
Pan troglodytes	ENSPTRG00000008362	2 retrocopies	retro_ptro_250, retro_ptro_2794,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,