RetrogeneDB ID: retro_amel_1871

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195022.1:74754..75162(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000014761
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COA1
• Ensembl ID: ENSAMEG00000009377
• Aliases: None
• Description: cytochrome c oxidase assembly factor 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21868]

Sequence

>retro_amel_1871
ATGCCATTGCCTCTGGGGAAACTGGTTCTTTTTTCCAGTGTGGTGGCCAGTGGGAGTTGTGCCCTCATATATTACCTTAT
ACAAAAAGCTTTTTCTGGGGCTTCCTATTACCAGCTGGCATTGGAGCACCTACACAGCTACCCTGAGGCCCTGGAGGTTC
TGTGCACTTCTCTCAACATCTACCATCTTCCCCTTACCAACAAGTACAACTTTGCCAACATTGCCAATGCCTAGTTGAAG
ATTCCTGTCTCTGGATCCAAGTCAGAGGGCTATCTCTATGTCAGCTCAACCAGAGATGCCCCCTTTCAGAGGTGGCACCT
TCAGGAGGTCTTCTTAAAGCTCAAGGATGGTCAGCAGATACCTGTGTTCAAATTCAGTGGGGACACTGGTGATGAAGTGA
AAAAGGAG

Alignment

ORF - retro_amel_1871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPWSLGKLAFSLSVVAGGSCTLTYYLIQKAFTKTSYYQLALEQLHSHPEALEALGAPLNVHYLHLIDRAN
          MP..LGKL....SVVA.GSC.L.YYLIQKAF...SYYQLALE.LHS.PEALE.L...LN...L.L....N
Retrocopy MPLPLGKLVLFSSVVASGSCALIYYLIQKAFSGASYYQLALEHLHSYPEALEVLCTSLNIYHLPLTNKYN

Parental  FVDIANAQLKIPVSGSKAEGHLHVSSSRHAPFQRWHLQEVFLKLEDGQQIPVFKVSGNTDHEVKKE
          F..IANA.LKIPVSGSK.EG.L.VSS.R.APFQRWHLQEVFLKL.DGQQIPVFK.SG.T..EVKKE
Retrocopy FANIANA*LKIPVSGSKSEGYLYVSSTRDAPFQRWHLQEVFLKLKDGQQIPVFKFSGDTGDEVKKE

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_1871 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1871 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009377	1 retrocopy	retro_amel_1871 ,
Canis familiaris	ENSCAFG00000031110	1 retrocopy	retro_cfam_2115,
Callithrix jacchus	ENSCJAG00000007826	1 retrocopy	retro_cjac_656,
Homo sapiens	ENSG00000106603	1 retrocopy	retro_hsap_2595,
Gorilla gorilla	ENSGGOG00000034928	1 retrocopy	retro_ggor_1624,
Macaca mulatta	ENSMMUG00000019023	1 retrocopy	retro_mmul_653,
Mustela putorius furo	ENSMPUG00000018149	1 retrocopy	retro_mputfur_1572,
Nomascus leucogenys	ENSNLEG00000003316	1 retrocopy	retro_nleu_1527,
Pongo abelii	ENSPPYG00000017606	1 retrocopy	retro_pabe_1914,
Pan troglodytes	ENSPTRG00000019125	1 retrocopy	retro_ptro_1520,