RetrogeneDB ID: retro_pabe_2445

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:81778119..81778350(+)
• Located in intron of: ENSPPYG00000014871

Retrocopy information

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

Parental gene information

• Parental gene symbol: MINOS1
• Ensembl ID: ENSPPYG00000001788
• Aliases: None
• Description: mitochondrial inner membrane organizing system 1 [Source:HGNC Symbol;Acc:32068]

Sequence

>retro_pabe_2445
TCAGAGCCAGAGCTCAGCAAGAAGTGAGAGCGGTGTTTGGCAGATGCGGTGGTAAAGATAGGTACTGGTTTGGAATTAGG
AATCGTTTTCTCACCTAAACTTCTTTAAAAGAAGAAAGTAGCCATTAGCCTTTAGTTTGGCATGGAATTGGGAATGGCCT
ACTCCAGCCATCGGCATAGTTTCCAGGCTCCATGTCTTCTATGCGGAACGTGTGTCAAAGAACAGGAGCAG

Alignment

ORF - retro_pabe_2445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.89 %
• Parental protein coverage: 60.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SESELGRKWDRCLADAVVKIGTGFGLGIVFS-LTFFKRRMWPLAFG-SGMGLGMAYSNCQHDFQAPYLLH
          SE.EL..K..RCLADAVVKIGTG..LGIVFS.L.FFKRR..PLAF...GM.LGMAYS...H.FQAP.LL.
Retrocopy SEPELSKK*ERCLADAVVKIGTGLELGIVFS>LNFFKRRK*PLAFS<FGMELGMAYSSHRHSFQAPCLLC

Parental  GKYVKEQEQ
          G..VKEQEQ
Retrocopy GTCVKEQEQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	68.84 RPM
SRP007412_cerebellum	0.00 RPM	41.95 RPM
SRP007412_heart	0.00 RPM	77.97 RPM
SRP007412_kidney	0.00 RPM	69.67 RPM
SRP007412_liver	0.00 RPM	25.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2445 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2445 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2445 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2948
Pan troglodytes	retro_ptro_2050
Gorilla gorilla	retro_ggor_2042
Macaca mulatta	retro_mmul_1949

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006709	1 retrocopy	retro_cjac_2070,
Echinops telfairi	ENSETEG00000010942	5 retrocopies	retro_etel_1360, retro_etel_1463, retro_etel_171, retro_etel_459, retro_etel_978,
Homo sapiens	ENSG00000173436	3 retrocopies	retro_hsap_1857, retro_hsap_2761, retro_hsap_2948,
Gallus gallus	ENSGALG00000004039	1 retrocopy	retro_ggal_19,
Gorilla gorilla	ENSGGOG00000007347	4 retrocopies	retro_ggor_1920, retro_ggor_2042, retro_ggor_2154, retro_ggor_979,
Macaca mulatta	ENSMMUG00000005855	2 retrocopies	retro_mmul_1268, retro_mmul_1949,
Mus musculus	ENSMUSG00000050608	1 retrocopy	retro_mmus_2357,
Nomascus leucogenys	ENSNLEG00000007867	2 retrocopies	retro_nleu_1297, retro_nleu_665,
Pongo abelii	ENSPPYG00000001788	3 retrocopies	retro_pabe_1513, retro_pabe_2251, retro_pabe_2445 ,
Pan troglodytes	ENSPTRG00000000269	2 retrocopies	retro_ptro_1868, retro_ptro_2050,
Rattus norvegicus	ENSRNOG00000042696	2 retrocopies	retro_rnor_16, retro_rnor_2460,
Tarsius syrichta	ENSTSYG00000002903	1 retrocopy	retro_tsyr_825,