RetrogeneDB ID: retro_nleu_994

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:24660275..24661617(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LPCAT2
• Ensembl ID: ENSNLEG00000001258
• Aliases: None
• Description: None

Sequence

>retro_nleu_994
ATTGCCTTCCTCTTCCTCTGGCCAGTGGCCATGCTTTCCACCTCTGGCTATCCTGCTCAAATCCTGCAACCCTGCCAAGA
GTTGGAGGAAAAAACTGGTGAAACCAGTACTCAAGCTCATGCTTCAGGTGGGTTTCTTTTTAGCTGGGTTCCTGGCTAAA
GTGAAAGGGAAAAAGGCAACCCAAGACAAGGCCCCTATCTTCGTTACAGCACCACGGTCCACTTTCTTTGACTCAATCCC
CTGTGTGGTGGTGGGGTTACCCTCAGTGGTCTCTGCAAGTCAAAACGTGCAGATCCCATTGGCTGGGAAATTCCTATGGT
CAACACAGCTGGTGCTTGTGATCTGAGAAGACCCTAATTCCAGGAAGAATACTAAGAATGAAATCCTGAAGTGAGCGACA
TTTGGAAAGAAGTGGCCACAGATTCTGATTTTCCTAGAAGGTGTGTGCACCAATCGCTACTGTCTAGTCACTTTTAAACT
AGGGGCCTTCTGTTCAGGTGATCCTGTGTAGCCAGTGCTGCTCAGGTACCCAAACACCCTGGACACGGCAATCTGGACCT
GGCAGGGATTTACAGCCTTCCAGGCCTGTATGTTGACACTCAGTCAACTCTTCACCAGGGTAGAAGTTGAGTTTATGCCT
GTTTATATCCCAAATGATGAAGAAAAAAAAGACCCCATCCTTTTTGCCAATACAGTACACATCAACATGGCAAATGCTCT
AGGGGTGCCTGGGACAGGGCACACTTATGAAGACTGCAGACTGATGATCTCCGCAGGTAACCTTCAACTACCCATAGAAG
CTGGTTTCGTGGAATTTACAAAAATTAGCCAGAAGTTGAAGTTAGATAGGGATAACATTCATCAGCATTTGGATGAATAT
GCTGCAATTGCCGTTGCCTCAAAAGGAGGGAAGATAGGAATTGAAGAATTTTCAAGTTATTTAAAACTCCCAACTTCAGA
GCCCTTGAGACAACCCCCTGCCCTCTTTGGCAGGAATAATGATGGCAGCATAGACTTCAGAGAGTATGTAATAGGTCTGA
CTGTTCTATGCAATCCTGCCAACATTGAAAAGGGTCTGCAAATGTCCTTTAAGCTTTTTGATCTTGATGCGGATGGTTTA
ATAACAGAGCAGCAGTTCGCTGCTATACTTCAGGCAGCTTTTGGAGTGCCAAATGTTGATGTTTCCAGGCTCTTTCAGGA
AATAGCTGGACAGAAATCAGTGTACATTTCATATGAGAGATTTAAGAAATTTGCCCTGAAGCATCCAGCATATCCCAAGT
TATTTAATTCACACCTAGACCTCCAGGCAGCCTATATATATTCATTGCCCCAAAAAGTACAG

Alignment

ORF - retro_nleu_994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.83 %
• Parental protein coverage: 81.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LILLLAWPFAAISTVCCPEKLT-HPVTGWRRKITQTALKFLARAMFFSMGFIVAVKGKIASPLEAPVFVA
          ...L..WP.A..ST...P......P...WR.K.....LK......FF..GF...VKGK.A....AP.FV.
Retrocopy IAFLFLWPVAMLSTSGYPAQIL>NPAKSWRKKLVKPVLKLMLQVGFFLAGFLAKVKGKKATQDKAPIFVT

Parental  APHSTFFDGIACVVAGLPSIVSRNENAQVPLIGRLLRAVQPVLVSRVDPDSRKNTINEIIKRTTSGGEWP
          AP.STFFD.I.CVV.GLPS.VS...N.Q.PL.G..L...Q.VLV...DP.SRKNT.NEI.K..T.G..WP
Retrocopy APRSTFFDSIPCVVVGLPSVVSASQNVQIPLAGKFLWSTQLVLVI*EDPNSRKNTKNEILK*ATFGKKWP

Parental  QILVFPEGTCTNRSCLITFKPGAFIPGVPVQPVLLRYPNKLDTVTWTWQGYTFIQLCMLTFCQLFTKVEI
          QIL.F.EG.CTNR.CL.TFK.GAF..G.PV.PVLLRYPN.LDT..WTWQG.T..Q.CMLT..QLFT.VE.
Retrocopy QILIFLEGVCTNRYCLVTFKLGAFCSGDPV*PVLLRYPNTLDTAIWTWQGFTAFQACMLTLSQLFTRVEV

Parental  EFMPVQVPNDEEKNDPVLFANKVRNLMAEALGIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFTKISRKL
          EFMPV..PNDE...DP.LFAN.V...MA.ALG.P.T.HTYEDCRLMISAG.L.LP.EAG.VEFTKIS.KL
Retrocopy EFMPVYIPNDEXXXDPILFANTVHINMANALGVPGTGHTYEDCRLMISAGNLQLPIEAGFVEFTKISQKL

Parental  KLDWDGVRKHLDEYASIASSSKGGRIGIEEFATYLKLPVSDVLRQLFALFDRNHDGSIDFREYVIGLAVL
          KLD.D....HLDEYA.IA..SKGG.IGIEEF..YLKLP.S..LRQ..ALF.RN.DGSIDFREYVIGL.VL
Retrocopy KLDRDNIHQHLDEYAAIAVASKGGKIGIEEFSSYLKLPTSEPLRQPPALFGRNNDGSIDFREYVIGLTVL

Parental  CNPSNTEEIIQVAFKLFDVDEDGYITEEEFSTILQASLGVPDLDVSGLFKEIAQGDSV--SYEEFKSFAL
          CNP.N.E...Q..FKLFD.D.DG.ITE..F..ILQA..GVP..DVS.LF.EIA...SV..SYE.FK.FAL
Retrocopy CNPANIEKGLQMSFKLFDLDADGLITEQQFAAILQAAFGVPNVDVSRLFQEIAGQKSVYISYERFKKFAL

Parental  KHPEYAKIFTTYLDLQTCHVFSLPKEVQ
          KHP.Y.K.F...LDLQ.....SLP..VQ
Retrocopy KHPAYPKLFNSHLDLQAAYIYSLPQKVQ

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_994 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.

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019272	1 retrocopy	retro_btau_64,
Callithrix jacchus	ENSCJAG00000012902	1 retrocopy	retro_cjac_2945,
Dasypus novemcinctus	ENSDNOG00000006859	1 retrocopy	retro_dnov_1735,
Dipodomys ordii	ENSDORG00000013193	1 retrocopy	retro_dord_399,
Equus caballus	ENSECAG00000009649	1 retrocopy	retro_ecab_865,
Erinaceus europaeus	ENSEEUG00000014277	1 retrocopy	retro_eeur_109,
Homo sapiens	ENSG00000087253	1 retrocopy	retro_hsap_185,
Gorilla gorilla	ENSGGOG00000005144	1 retrocopy	retro_ggor_266,
Loxodonta africana	ENSLAFG00000003965	1 retrocopy	retro_lafr_66,
Myotis lucifugus	ENSMLUG00000004008	1 retrocopy	retro_mluc_88,
Macaca mulatta	ENSMMUG00000004478	1 retrocopy	retro_mmul_392,
Mus musculus	ENSMUSG00000033192	1 retrocopy	retro_mmus_270,
Nomascus leucogenys	ENSNLEG00000001258	1 retrocopy	retro_nleu_994 ,
Pongo abelii	ENSPPYG00000007358	1 retrocopy	retro_pabe_445,
Pan troglodytes	ENSPTRG00000008124	2 retrocopies	retro_ptro_171, retro_ptro_2928,
Pteropus vampyrus	ENSPVAG00000007801	1 retrocopy	retro_pvam_173,
Rattus norvegicus	ENSRNOG00000016643	1 retrocopy	retro_rnor_309,
Sorex araneus	ENSSARG00000011914	1 retrocopy	retro_sara_88,
Sarcophilus harrisii	ENSSHAG00000012383	1 retrocopy	retro_shar_116,
Tursiops truncatus	ENSTTRG00000001182	1 retrocopy	retro_ttru_188,