RetrogeneDB ID: retro_pabe_1363

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:59799554..59800428(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5A1
• Ensembl ID: ENSPPYG00000009130
• Aliases: None
• Description: ATP synthase subunit alpha, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001126846]

Sequence

>retro_pabe_1363
AGACTTACAGATGTAGATGCCGTGAAGTACACCACTGTGGTGTCAGCTATGGCCTCAGATGCTGCCCTACTTCAGTACCT
GGCTCCTTACTCTGACTGTTCCATGGGAGAGTATTTTAGAGACGATGGCAAATATACTTTGATCATCTATGACGACTTAT
CCAAACAGGCTGTCGCTTACCGTCAGATGTCTCTGTTGTTCCACCAACCCCCTGGTCGTAAGGCCTGTCCTGGTGATGTG
TTTTACCTACACTCCCAGTTGCTGGAGAGAGCAGCCAAAATGAATGATGCTTTTGTTGGTGGCTCCTTGACTGCTTTGCT
AGTCGTAGAAACACAGGCTGGTGACGTGTCTGCTTACATTCCAACGAATGTCATTTCCATCACTGACAGACAGATCTTCT
TGGAAACAGAATTGTTCTACAAAGATATCCGCTCTGCCATTAACATTGGTCTGTCTGTGTCTCGTGTTGGATCTGCTGCC
CAAACCAGGACTATGAAGCAGGTGGCAGGTACCATAAGCTGGAATTGGCTCAGTATCGTGAGGTTGCTGCTTTTGCCCAG
TTTGGTTTTGACCTCGATGCTCCCACTCAAAACTTTTGAGTCGTGGTGTGCATCTAACTGAGTTGCTGAAGCAAGGACGG
TATTCTCCCATGGTTATTGAAGAACAAGTGGCTGTTACCTATGCGGGTGTAAGGGGGTATCTTGATAAACTGGAGCCCAG
CAAGATTACAAAGTTTGAGAATGGTTTCTTGTCTCATGTTGTCAGCCAGCACTAAGCTCTGTTGGGCACTATCAGGGCTG
ATGGAAAGATCTCAGAAGACTCAGATGCAAAGCTGACGGAGATTGTAACAAACTTATTGGCTGGATTTGAAGCT

Alignment

ORF - retro_pabe_1363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.07 %
• Parental protein coverage: 52.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRP
          RLTD.DA.KYT.VVSA.ASDAA.LQYLAPYS.CSMGEYFRD.GK..LIIYDDLSKQAVAYRQMSLL...P
Retrocopy RLTDVDAVKYTTVVSAMASDAALLQYLAPYSDCSMGEYFRDDGKYTLIIYDDLSKQAVAYRQMSLLFHQP

Parental  PGREAYPGDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFY
          PGR.A.PGDVFYLHS.LLERAAKMNDAF.GGSLTAL.V.ETQAGDVSAYIPTNVISITD.QIFLETELFY
Retrocopy PGRKACPGDVFYLHSQLLERAAKMNDAFVGGSLTALLVVETQAGDVSAYIPTNVISITDRQIFLETELFY

Parental  KGIRPAINVGLSVSRVGSAAQTRAMKQVAGTM-KLELAQYREVAAFAQFGSDLDAATQ-QLLSRGVRLTE
          K.IR.AIN.GLSVSRVGSAAQTR.MKQVAGT..KLELAQYREVAAFAQFG.DLDA.TQ..LLSRGV.LTE
Retrocopy KDIRSAINIGLSVSRVGSAAQTRTMKQVAGTI<KLELAQYREVAAFAQFGFDLDAPTQ<KLLSRGVHLTE

Parental  LLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVVSQHQALLGTIRADGKISEQSDAK
          LLKQG.YSPM.IEEQVAV.YAGVRGYLDKLEPSKITKFEN.FLSHVVSQH.ALLGTIRADGKISE.SDAK
Retrocopy LLKQGRYSPMVIEEQVAVTYAGVRGYLDKLEPSKITKFENGFLSHVVSQH*ALLGTIRADGKISEDSDAK

Parental  LKEIVTNFLAGFEA
          L.EIVTN.LAGFEA
Retrocopy LTEIVTNLLAGFEA

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	343.80 RPM
SRP007412_cerebellum	0.12 RPM	283.94 RPM
SRP007412_heart	0.03 RPM	1006.12 RPM
SRP007412_kidney	0.00 RPM	514.77 RPM
SRP007412_liver	0.09 RPM	194.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1363 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1363 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1363 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1702
Pan troglodytes	retro_ptro_1151
Gorilla gorilla	retro_ggor_1275

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002507	2 retrocopies	retro_btau_1380, retro_btau_1426,
Canis familiaris	ENSCAFG00000017648	2 retrocopies	retro_cfam_1483, retro_cfam_516,
Dasypus novemcinctus	ENSDNOG00000006331	2 retrocopies	retro_dnov_1740, retro_dnov_2525,
Equus caballus	ENSECAG00000021561	1 retrocopy	retro_ecab_788,
Homo sapiens	ENSG00000152234	1 retrocopy	retro_hsap_1702,
Gorilla gorilla	ENSGGOG00000016560	1 retrocopy	retro_ggor_1275,
Meleagris gallopavo	ENSMGAG00000009963	1 retrocopy	retro_mgal_14,
Microcebus murinus	ENSMICG00000017500	1 retrocopy	retro_mmur_1210,
Myotis lucifugus	ENSMLUG00000009856	1 retrocopy	retro_mluc_1198,
Macaca mulatta	ENSMMUG00000003570	1 retrocopy	retro_mmul_1208,
Mustela putorius furo	ENSMPUG00000000923	1 retrocopy	retro_mputfur_601,
Nomascus leucogenys	ENSNLEG00000010973	1 retrocopy	retro_nleu_1334,
Pongo abelii	ENSPPYG00000009130	1 retrocopy	retro_pabe_1363 ,
Pan troglodytes	ENSPTRG00000009991	1 retrocopy	retro_ptro_1151,
Sarcophilus harrisii	ENSSHAG00000017177	1 retrocopy	retro_shar_109,
Tarsius syrichta	ENSTSYG00000007804	1 retrocopy	retro_tsyr_1186,
Tursiops truncatus	ENSTTRG00000005118	1 retrocopy	retro_ttru_159,