RetrogeneDB ID: retro_pabe_2247

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:114636836..114637468(+)
• Located in intron of: ENSPPYG00000014042

Retrocopy information

• Ensembl ID: ENSPPYG00000014043
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP5O
• Ensembl ID: ENSPPYG00000011384
• Aliases: None
• Description: ATP synthase subunit O, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001125158]

Sequence

>retro_pabe_2247
ATGGCTGCCCCAGCAGTGTCCGGGCTCTCCTGGCAGGTGGATGTTTCAGTACCTCTGTGGTCAGACCATTTGCCAAGCTT
GTGAGGCCTCCTGTTCAGGTATACGGTATTGAAGGTCACTATGCCACCACTCTTTATTCTGCTGCATCAAAACAGAATAA
GCTGGAGCAAGTAGAAAAGGAGTTGTTGAGAGTAGCACAAATCCTGAAGGAACCCAAAGTGGCTGCTTCTGTTTTGAATC
CCTATGTGAAGCGTTCCATTAAAGTGAAAAGCCTAAATGACATCACAGCAAAAGAGAGGTTCTCTCCCCTTACCACCAAC
CTGATCAATTTGCTTGCTGAAAATGGTCGATTAAGCAATACCCAAGGAGTCATTTCTGCCTTTTCTGCCATGATGAGTGT
CCATTGCGGAGAGGTGCCTTGCACAGTGACCTCTGCATCTCCTTTAGAAGAAGCCACACTCTCTGAATTAAAAACTGTCC
TTAAGAGCTTCCTAAGTCAAGGCCAAGTATTGAAATTGGAGGCTAAGACTGATCCGTCAGTCTTGGGTGGAATGATTGTG
CGCATTGGAGAGAAATATGTTGACATGTCTGTCAAGACCAAGATTCAGAAGCTGGGAAGGGCTATGCGGGAG

Alignment

ORF - retro_pabe_2247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.34 %
• Parental protein coverage: 99.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATPAVSGLSRQVR-CFSTSVVRPFAKLVRPPVQVYGIEGRYATALYSAASKQNKLEQVEKELLRVAQIL
          MA.PAVSGLS.QV..CFSTSVVRPFAKLVRPPVQVYGIEG.YAT.LYSAASKQNKLEQVEKELLRVAQIL
Retrocopy MAAPAVSGLSWQVD<CFSTSVVRPFAKLVRPPVQVYGIEGHYATTLYSAASKQNKLEQVEKELLRVAQIL

Parental  KEPKVAASVLNPYVKHSIKVKSLNDITAKERFSPLTTNLINLLAENGRLSNTQGVVSAFSTMMSVHRGEV
          KEPKVAASVLNPYVK.SIKVKSLNDITAKERFSPLTTNLINLLAENGRLSNTQGV.SAFS.MMSVH.GEV
Retrocopy KEPKVAASVLNPYVKRSIKVKSLNDITAKERFSPLTTNLINLLAENGRLSNTQGVISAFSAMMSVHCGEV

Parental  PCTVTSASPLEEATLSELKTVLKSFLSQGQVLKLEAKTDPSILGGMIVRIGEKYVDMSVKTKIQKLSRAM
          PCTVTSASPLEEATLSELKTVLKSFLSQGQVLKLEAKTDPS.LGGMIVRIGEKYVDMSVKTKIQKL.RAM
Retrocopy PCTVTSASPLEEATLSELKTVLKSFLSQGQVLKLEAKTDPSVLGGMIVRIGEKYVDMSVKTKIQKLGRAM

Parental  RE
          RE
Retrocopy RE

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	4.26 RPM	49.71 RPM
SRP007412_cerebellum	4.26 RPM	73.93 RPM
SRP007412_heart	9.63 RPM	112.47 RPM
SRP007412_kidney	6.10 RPM	59.96 RPM
SRP007412_liver	3.89 RPM	48.44 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2247 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2247 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2247 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014708	1 retrocopy	retro_amel_1914,
Canis familiaris	ENSCAFG00000009541	3 retrocopies	retro_cfam_1277, retro_cfam_2198, retro_cfam_235,
Choloepus hoffmanni	ENSCHOG00000011242	1 retrocopy	retro_chof_638,
Callithrix jacchus	ENSCJAG00000002873	1 retrocopy	retro_cjac_1567,
Equus caballus	ENSECAG00000009059	1 retrocopy	retro_ecab_633,
Echinops telfairi	ENSETEG00000000807	5 retrocopies	retro_etel_1412, retro_etel_1906, retro_etel_507, retro_etel_839, retro_etel_841,
Felis catus	ENSFCAG00000028656	1 retrocopy	retro_fcat_1511,
Homo sapiens	ENSG00000241837	1 retrocopy	retro_hsap_2377,
Gorilla gorilla	ENSGGOG00000012611	1 retrocopy	retro_ggor_1803,
Macropus eugenii	ENSMEUG00000006613	4 retrocopies	retro_meug_122, retro_meug_1552, retro_meug_381, retro_meug_805,
Myotis lucifugus	ENSMLUG00000008224	3 retrocopies	retro_mluc_1833, retro_mluc_826, retro_mluc_856,
Macaca mulatta	ENSMMUG00000015504	1 retrocopy	retro_mmul_253,
Monodelphis domestica	ENSMODG00000021057	2 retrocopies	retro_mdom_280, retro_mdom_95,
Mustela putorius furo	ENSMPUG00000001319	5 retrocopies	retro_mputfur_1593, retro_mputfur_1628, retro_mputfur_1639, retro_mputfur_581, retro_mputfur_918,
Mus musculus	ENSMUSG00000022956	2 retrocopies	retro_mmus_2196, retro_mmus_955,
Otolemur garnettii	ENSOGAG00000015850	4 retrocopies	retro_ogar_3518, retro_ogar_418, retro_ogar_559, retro_ogar_944,
Pongo abelii	ENSPPYG00000011384	1 retrocopy	retro_pabe_2247 ,
Pan troglodytes	ENSPTRG00000013876	1 retrocopy	retro_ptro_1739,
Rattus norvegicus	ENSRNOG00000001991	1 retrocopy	retro_rnor_2210,
Sarcophilus harrisii	ENSSHAG00000000409	3 retrocopies	retro_shar_369, retro_shar_389, retro_shar_668,
Sus scrofa	ENSSSCG00000012042	2 retrocopies	retro_sscr_226, retro_sscr_566,
Ictidomys tridecemlineatus	ENSSTOG00000008658	3 retrocopies	retro_itri_1030, retro_itri_565, retro_itri_794,