RetrogeneDB ID: retro_pabe_177

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:38010836..38011502(-)
• Located in intron of: ENSPPYG00000018510

Retrocopy information

• Ensembl ID: ENSPPYG00000018511
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CXorf56
• Ensembl ID: ENSPPYG00000020670
• Aliases: None
• Description: UPF0428 protein CXorf56 homolog [Source:RefSeq peptide;Acc:NP_001125661]

Sequence

>retro_pabe_177
ATGCCGAAAGTAGTGTCTCGGTCAGTAGTCTGCTCTGACACTCGGGACCGGGAGGAATATGACGACGGTGAGAAGCCCCT
CCATGTGTACTACTGTTTGTGCGGCCACGTGGTCCTAGTGCTGGACTGTCAGTTAGAGAAATTGCCCATGAGGCCCCGGG
ACCGGTCCCGTGTGATTGATGCTGCCAAACATGCCCATAAGTTTTGTAACACAGAAGACGAAGAGACTATGTATCTGCGG
AGACCTGAAGGCATTGAACTACAGTACAGAAAGAAATGTGCAAAATGTGGACTGCTGCTCTTTTACCAATCCCAGCCGAA
GAATGCTCCCGTTACCTTCATTGTGGATGGAGCAGTAGTCAAGTTTGGCCAGGGCTTTGGGAAAACGAACATATATACTC
AGAAACAAGAGCCTCCTAAGAAGGTGATGATGACCAAACGGACCAAAGACATGGGCAAGTTCAGTTCTGTCACTGTGTCT
ACCATTGATGAAGAGGAAGAGGAGATTGAGGCTAGGGAAGTTGCTGACTCGTATGCACAGAATGCCAAAGTGATTGAAAA
ACAGCTGGAGCGCAAAGGCATGAGCAAGAGGCCACTGCAAGAGCTGGCTGAATGGGAAGCCAAGAAAGTGAAAATGAAGG
GGACCTTGATTGACAACCAGTTCAAA

Alignment

ORF - retro_pabe_177 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQMVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN
          MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCG..VLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN
Retrocopy MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGHVVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN

Parental  TEDEETMYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
          TEDEETMYLRRPEGIE.QYRKKCAKCGL.LFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
Retrocopy TEDEETMYLRRPEGIELQYRKKCAKCGLLLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK

Parental  KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRRLQELAELEAKKA
          KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKR.LQELAE.EAKK.
Retrocopy KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRPLQELAEWEAKKV

Parental  KMKGTLIDNQFK
          KMKGTLIDNQFK
Retrocopy KMKGTLIDNQFK

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	0.66 RPM	11.06 RPM
SRP007412_cerebellum	0.24 RPM	7.90 RPM
SRP007412_heart	0.09 RPM	2.38 RPM
SRP007412_kidney	0.46 RPM	8.35 RPM
SRP007412_liver	0.09 RPM	3.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_177 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_177 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4044
Pan troglodytes	retro_ptro_104
Gorilla gorilla	retro_ggor_2711

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005111	1 retrocopy	retro_cjac_311,
Homo sapiens	ENSG00000018610	1 retrocopy	retro_hsap_4044,
Gorilla gorilla	ENSGGOG00000013324	1 retrocopy	retro_ggor_2711,
Latimeria chalumnae	ENSLACG00000012468	1 retrocopy	retro_lcha_59,
Myotis lucifugus	ENSMLUG00000015751	1 retrocopy	retro_mluc_72,
Macaca mulatta	ENSMMUG00000022665	1 retrocopy	retro_mmul_2333,
Mus musculus	ENSMUSG00000006423	1 retrocopy	retro_mmus_1715,
Nomascus leucogenys	ENSNLEG00000014862	1 retrocopy	retro_nleu_2057,
Otolemur garnettii	ENSOGAG00000012474	1 retrocopy	retro_ogar_145,
Pongo abelii	ENSPPYG00000020670	1 retrocopy	retro_pabe_177 ,
Pan troglodytes	ENSPTRG00000022224	1 retrocopy	retro_ptro_104,
Sorex araneus	ENSSARG00000003163	1 retrocopy	retro_sara_5,
Sarcophilus harrisii	ENSSHAG00000006319	1 retrocopy	retro_shar_16,
Ictidomys tridecemlineatus	ENSSTOG00000011579	1 retrocopy	retro_itri_103,
Tarsius syrichta	ENSTSYG00000008043	1 retrocopy	retro_tsyr_634,
Tursiops truncatus	ENSTTRG00000013101	2 retrocopies	retro_ttru_231, retro_ttru_77,