RetrogeneDB ID: retro_nleu_1334

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397289.1:25143448..25144730(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5A1
• Ensembl ID: ENSNLEG00000010973
• Aliases: None
• Description: ATP synthase subunit alpha [Source:UniProtKB/TrEMBL;Acc:G1RK60]

Sequence

>retro_nleu_1334
AAGGAAGGAGGTATAGTGAAGAGGACAGGAACCTTTGTGGATGTTCCAGTCGGTGAGGAGCTGTTGGGTCGTGTAGTTGA
TGCTCTTGGTAATGCTATTGATGGAAAGGGTCCAGTTGGTTCCAAGACCCATAAGTGAGTCGGTCTGAAAGCCCCCAGAA
TCATTCCTCGAACTTCAGTGCAGGAACCAATGCCGACTGGCATTAAGACTGTGGATAGCTTGGTGCCAATTGGTCATGGT
CAGCATGAGCTGATTATTGGTGACCGAAAGACTGGGAAAACCTCAATTGCTATTGACACAATCATTAACCAGAAACATTT
CAATGATAGATCTGAAGAAAAGAAGAAGCTGTACTGTATCTATGTTGCTATTGGTCAAAAGAGATCCACTGTTGCTCAGT
TGGTGAAGAGACTTACAGATGCAGATGCCGTGAAGTACACCATTGTGGTGTCAGCTGCAGGCTCAGATGCTGCCCTACTT
CAGTACCTGGCTCCTTACTCTGACTGTTCCATGGGAGAGTATTTTAGAGATGATGGCAAATATTCTTTGATCATCTGTGA
CGACTTATCCAAACAGGCTGTTGCTTACCGTCAGATGTCTCTGTTGCTCCACCGACCCCCTGATCGTAAGGCCTGTCCTG
GTGATGTGTTTTACCTACACTCCCAGTTGCTGAAGAGAGCAGCCAAAATGAATGATGCTTTTGGTGGTGGCTCCTTGACT
GCTTTGCTAGTCATAGAAACACAGGCTGGTGATGTGTCTGCTTACATTCCAACGAATGTCATTTCCATCACTGACAGACA
GATCTTCTTGGAAACAGAATTGTTCTACAGAGATATCCGCTCTGCCGTTAACATTGGTCTGTCTGTGTCTCGTGTTGGAT
CTGCTGCCCAAACCAGGACTATGAAGCAGGTGGCAGGTACCATAAGCTGGAATTGGCTCAGTACTGTGAAGTTGCTGCTT
TTGCCCAGTTTGGTTCTGACCTCGATGCTCCCACTCAACAACTTTTAAGTCGTGGTGTGCATCTAACTGAGTTGCTGAAG
CAAGGACAGTATTCTCCCACGGTTATTGAAGAACAAGTGGCTGTTATCTATGCGGGTGTAAGGGGGTATCTTGATAAACT
GGAGCCCAGCAAGATCACAAAGTTTGAGAATGCTTTCTTGTCTCATGTTGTCAGCCAGCACTAAGCCCTGTTGGCACTAT
CAGGGCTGATGGAAAGATCTCAGAAGACTCAGATGCAAAGCTGACGGAGATTGTAACAAACTTCTTGGCTGGATTTGAAG
CT

Alignment

ORF - retro_nleu_1334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.08 %
• Parental protein coverage: 77.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKTRRRVGLKAPGIIPRISVREPMQTGIKA
          KEG.IVKRTG..VDVPVGEELLGRVVDALGNAIDGKGP.GSKT...VGLKAP.IIPR.SV.EPM.TGIK.
Retrocopy KEGGIVKRTGTFVDVPVGEELLGRVVDALGNAIDGKGPVGSKTHK*VGLKAPRIIPRTSVQEPMPTGIKT

Parental  VDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGSDEKKKLYCIYVAIGQKRSTVAQLVKRLTD
          VDSLVPIG.GQ.ELIIGDR.TGKTSIAIDTIINQK.FND.S.EKKKLYCIYVAIGQKRSTVAQLVKRLTD
Retrocopy VDSLVPIGHGQHELIIGDRKTGKTSIAIDTIINQKHFNDRSEEKKKLYCIYVAIGQKRSTVAQLVKRLTD

Parental  ADAMKYTIVVSATASDAAPLQYLAPYSGCSIGRVFLETMGKHTLIIYDDLSQTAVAYRQMSLLLRRPPGR
          ADA.KYTIVVSA..SDAA.LQYLAPYS.CS.G..F....GK..LII.DDLS..AVAYRQMSLLL.RPP.R
Retrocopy ADAVKYTIVVSAAGSDAALLQYLAPYSDCSMGEYFRDD-GKYSLIICDDLSKQAVAYRQMSLLLHRPPDR

Parental  EAYPGDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGI
          .A.PGDVFYLHS.LL.RAAKMNDAFGGGSLTAL.VIETQAGDVSAYIPTNVISITD.QIFLETELFY..I
Retrocopy KACPGDVFYLHSQLLKRAAKMNDAFGGGSLTALLVIETQAGDVSAYIPTNVISITDRQIFLETELFYRDI

Parental  RPAINVGLSVSRVGSAAQTRAMKQVAGTM-KLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQ
          R.A.N.GLSVSRVGSAAQTR.MKQVAGT..KLELAQY.EVAAFAQFGSDLDA.TQQLLSRGV.LTELLKQ
Retrocopy RSAVNIGLSVSRVGSAAQTRTMKQVAGTI<KLELAQYCEVAAFAQFGSDLDAPTQQLLSRGVHLTELLKQ

Parental  GQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVVSQHQALL-GTIRADGKISEQSDAKLKE
          GQYSP..IEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVVSQH.ALL.GTIRADGKISE.SDAKL.E
Retrocopy GQYSPTVIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVVSQH*ALL<GTIRADGKISEDSDAKLTE

Parental  IVTNFLAGFEA
          IVTNFLAGFEA
Retrocopy IVTNFLAGFEA

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1334 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 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,