RetrogeneDB ID: retro_amel_1239

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193083.1:8161..8386(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000002166
• Aliases: None
• Description: None

Sequence

>retro_amel_1239
CCCCTCAATCCCGAACCTTTCCTCAATGGACTACCAGGAAGGCCAGTAATGGGGGAACTTCAGTGGGGAATGGAGTGCAA
AGGCTCCCTGGTACTTGTAGGTGGCTATATGAACATGCAGCTGGCAAACGTAAAAGAACGCATAGATGGAATATTGTCTG
GACGTTTGAGTGAGGTTTTAATAAAGCGTAATAATGTTTTTTATATCAGGAGTACTGAAGAAGAG

Alignment

ORF - retro_amel_1239 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.0 %
• Parental protein coverage: 88.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIR
          PLNP.PFLNGL.G.PVM..L.WGME.KG.LV.V.GYMNMQLAN..E.IDG.LSG.L.EVLI..NNV.YIR
Retrocopy PLNPEPFLNGLPGRPVMGELQWGMECKGSLVLVGGYMNMQLANVKERIDGILSGRLSEVLIKRNNVFYIR

Parental  GVEEE
          ..EEE
Retrocopy STEEE

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_1239 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1239 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 24 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239 , retro_amel_42, retro_amel_883,
Bos taurus	ENSBTAG00000016271	1 retrocopy	retro_btau_765,
Canis familiaris	ENSCAFG00000006395	6 retrocopies	retro_cfam_110, retro_cfam_1975, retro_cfam_372, retro_cfam_619, retro_cfam_742, retro_cfam_763,
Callithrix jacchus	ENSCJAG00000002705	2 retrocopies	retro_cjac_1705, retro_cjac_3039,
Equus caballus	ENSECAG00000019817	1 retrocopy	retro_ecab_154,
Erinaceus europaeus	ENSEEUG00000013509	4 retrocopies	retro_eeur_241, retro_eeur_465, retro_eeur_467, retro_eeur_636,
Echinops telfairi	ENSETEG00000001558	3 retrocopies	retro_etel_1765, retro_etel_1846, retro_etel_560,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Homo sapiens	ENSG00000139343	3 retrocopies	retro_hsap_125, retro_hsap_2487, retro_hsap_2645,
Gorilla gorilla	ENSGGOG00000001127	2 retrocopies	retro_ggor_1549, retro_ggor_225,
Latimeria chalumnae	ENSLACG00000002456	1 retrocopy	retro_lcha_73,
Loxodonta africana	ENSLAFG00000017426	1 retrocopy	retro_lafr_241,
Macaca mulatta	ENSMMUG00000009302	4 retrocopies	retro_mmul_1521, retro_mmul_361, retro_mmul_550, retro_mmul_893,
Monodelphis domestica	ENSMODG00000008091	3 retrocopies	retro_mdom_550, retro_mdom_780, retro_mdom_811,
Mustela putorius furo	ENSMPUG00000007176	3 retrocopies	retro_mputfur_1309, retro_mputfur_377, retro_mputfur_941,
Mus musculus	ENSMUSG00000020018	4 retrocopies	retro_mmus_1060, retro_mmus_1197, retro_mmus_2537, retro_mmus_3210,
Nomascus leucogenys	ENSNLEG00000005835	3 retrocopies	retro_nleu_2259, retro_nleu_274, retro_nleu_651,
Pongo abelii	ENSPPYG00000004847	2 retrocopies	retro_pabe_381, retro_pabe_489,
Pelodiscus sinensis	ENSPSIG00000016462	2 retrocopies	retro_psin_31, retro_psin_54,
Pteropus vampyrus	ENSPVAG00000009036	1 retrocopy	retro_pvam_1170,
Rattus norvegicus	ENSRNOG00000005556	4 retrocopies	retro_rnor_1822, retro_rnor_1849, retro_rnor_2926, retro_rnor_444,
Sarcophilus harrisii	ENSSHAG00000012294	1 retrocopy	retro_shar_468,
Sus scrofa	ENSSSCG00000000895	1 retrocopy	retro_sscr_958,
Tarsius syrichta	ENSTSYG00000006837	4 retrocopies	retro_tsyr_1239, retro_tsyr_1782, retro_tsyr_192, retro_tsyr_2115,