RetrogeneDB ID: retro_amel_257

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192368.1:2151917..2152234(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL40
• Ensembl ID: ENSAMEG00000011421
• Aliases: None
• Description: mitochondrial ribosomal protein L40 [Source:HGNC Symbol;Acc:14491]

Sequence

>retro_amel_257
CGCGGAGCTGGCTGGCTTCTGGGAACTTGGCGGACACAGAGCAGAGACATCCACCAGCGAGCTTCATTGTTGTCCTGGGA
AGTCGTTCCCATGAGAGCAAAAACCTCAGGCAAAGAAGAAAAAGGCAGATCCTAACAAAGACCAAGCAGCAAGGACCGCT
GGAAAAAGAGGATCCGACCACGGGAGAAAGCTGGCCGGGAGCGCATTCTCACTGGAAATGTTAGGAGACCCGTGAGGCTC
TTGGATAAAGCAGGGCAGCGGCCTCACGTGGAGCTCGCCTCTGAGGGCCTGAGCGGAGAGCTCTGCTTCTGGAAGAG

Alignment

ORF - retro_amel_257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.82 %
• Parental protein coverage: 51.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RSRSWPLGIWQTQIRDTHQRASLLSFWELIPMRAE-PLRKKKRVDPKKDQAV-KDRLKKRIRRLEKASQE
          R...W.LG.W.TQ.RD.HQRASLLS.WE..PMRA..P..KKK..DP.KDQA..KDR.KKRIR..EKA..E
Retrocopy RGAGWLLGTWRTQSRDIHQRASLLS-WEVVPMRAK>PQAKKKKADPNKDQAA<KDRWKKRIRPREKAGRE

Parental  LIPIEDFITPARLLDKARQRPHVELPFE-ESERRALLLKK
          .I.......P.RLLDKA.QRPHVEL..E...ERRALLL..
Retrocopy RILTGNVRRPVRLLDKAGQRPHVELASE<GPERRALLLEE

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_257 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_257 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001053	1 retrocopy	retro_acar_149,
Ailuropoda melanoleuca	ENSAMEG00000011421	1 retrocopy	retro_amel_257 ,
Callithrix jacchus	ENSCJAG00000001584	1 retrocopy	retro_cjac_3220,
Equus caballus	ENSECAG00000009876	1 retrocopy	retro_ecab_687,
Homo sapiens	ENSG00000185608	1 retrocopy	retro_hsap_1020,
Gorilla gorilla	ENSGGOG00000012336	1 retrocopy	retro_ggor_807,
Myotis lucifugus	ENSMLUG00000002456	1 retrocopy	retro_mluc_1950,
Macaca mulatta	ENSMMUG00000016081	1 retrocopy	retro_mmul_57,
Mustela putorius furo	ENSMPUG00000003865	1 retrocopy	retro_mputfur_394,
Nomascus leucogenys	ENSNLEG00000005372	1 retrocopy	retro_nleu_899,
Pongo abelii	ENSPPYG00000011578	1 retrocopy	retro_pabe_857,
Rattus norvegicus	ENSRNOG00000049686	1 retrocopy	retro_rnor_1624,
Tarsius syrichta	ENSTSYG00000014747	1 retrocopy	retro_tsyr_1589,