RetrogeneDB ID: retro_nleu_1780

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397308.1:16760245..16760962(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRIM1
• Ensembl ID: ENSNLEG00000017443
• Aliases: None
• Description: DNA primase [Source:UniProtKB/TrEMBL;Acc:G1S6M9]

Sequence

>retro_nleu_1780
TACAGCAGAGTGATAAAGAATTACGCCCAACACTGTGAATTTTCATTCACATTGAAAGATGACATTACATCCGATACCAA
TCCTTCAACAACCAGAGTGATCTGGAAAAGGAGATGCAGAAAATGAATCCATACAAGATTGATACAGGTGCAGTATATTC
CCACAGACCCAATCAACACAATACAGTGACGCTGGGAGCTTTCCAGGCTCAGGAAAAAGAACTGGTGTTGGACACTGACA
TGACAGACTATGACAATGTGAGGAGATGCTGTAGTTCTGCAGATACATGTTCTAAGTGCTGGAGCCTCATGACAAGGGCC
ATACGCAACACCAACACTACACTGAAGGAGGACTTTGGATTTAAGCCTCGTCTCCGGGTATATTCTGGAAGGAGGGGTGT
ACATTTTTCGGTCTGTGATAAATCACTTAGAAAACTGTCTTCGGTGGTATATTCTGGGATAGTTGAGTATTTGAGCCTTG
TAAAGCATAGTCAAGATGTTAAAAAGAAAGTTCACCTAACTGAAAAAAATTCACCCTTTTGTCAGAAAATCTATAAACAT
AATAAAAAACTTTGAAGAATATGCCTTGGTTAATCAAGATATTCTCAAAAATAACAAAAGCTGGGATAATATTTTAGCCC
TTGTTCCTGAAACAATTCAGGATGAACTTCAACAAAGGTTCCAAAAGTCTCACAATTCACTTCAGCATTGGGAGCAC

Alignment

ORF - retro_nleu_1780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 60.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YFAVIKNYFQHREFSFTLKDDI-YIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQ
          Y..VIKNY.QH.EFSFTLKDDI.YIRYQSFNNQSDLEKEMQKMNPYKID.GAVYSHRPNQHNTV.LGAFQ
Retrocopy YSRVIKNYAQHCEFSFTLKDDI<YIRYQSFNNQSDLEKEMQKMNPYKIDTGAVYSHRPNQHNTVTLGAFQ

Parental  AQEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMIMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVC
          AQEKELV.D.DMTDYD.VRRCCSSAD.C.KCW.LM..AIR.....LKEDFGFK.RL.VYSGRRGVH..VC
Retrocopy AQEKELVLDTDMTDYDNVRRCCSSADTCSKCWSLMTRAIRNTNTTLKEDFGFKPRLRVYSGRRGVHFSVC

Parental  DESVRKLSSAVRSGIVEYLSLVKGGQEVKKKVHLSE-KIHPFIRKSINIIKKYFEEYALVNQDILENKES
          D.S.RKLSS.V.SGIVEYLSLVK..Q.VKKKVHL.E.KIHPF.RKSINIIK..FEEYALVNQDIL.N..S
Retrocopy DKSLRKLSSVVYSGIVEYLSLVKHSQDVKKKVHLTE>KIHPFVRKSINIIKN-FEEYALVNQDILKNNKS

Parental  WDKILALVPETIHDELQQNFQKSHSSLQRWEH
          WD.ILALVPETI.DELQQ.FQKSH.SLQ.WEH
Retrocopy WDNILALVPETIQDELQQRFQKSHNSLQHWEH

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_1780 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780 ,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153, retro_pvam_703,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352,