RetrogeneDB ID: retro_ggor_266

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:94496483..94497822(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LPCAT2
• Ensembl ID: ENSGGOG00000005144
• Aliases: None
• Description: None

Sequence

>retro_ggor_266
ATTGCCTTCCTCTTCATCTGGCCAGTGGCCATGCTTTCCACCTTTGGCTATCCTGCTCAAATCCTGCAACCCTGCCAAGA
GTTGGAGAAAAAAAACTGGTGAAACCAGTACTCAAGCTCATGCTTCAGGTGGCTTTCTTTTTACCTGGGTTCCTGGCTAA
AGTGAAAGGGAAAAAGGCAACCCAAGACAAGGCCCCTATCTTCGTTACAGCACCACGGTCCACTTTCTTTGACTCATTCC
CCTGTGTGGTGGCAGGGTTACCCTCAGTGGTCTCTGCAAGTCAAAATGTGCAGATCCCATTGGCTGGGAAAGTCCTACTG
TCAACACAGCTGCTGCTTGTGATTTGAGAAGACCCCCATTCCAGGAAGAATACTAAGGATGAAATCCTGAAGTGAGTGAC
ATTTGGAAAGAAGTGGCCACAGATTCTGATTTTCCTAGGTGTGTGCATCAATTGGCCCGTCTAGTCATTTTTAAACTAGG
GGCCTTCTGTCCAGGTGTTCCTGTGTAGCCAGTGCTGCTCAGGTACCCAAACACCCTGGACATGGCAATCTGGACCTGGC
AGGGATTCACAGCCTTCCAGGCCTGTATGTTGACACTCAGTCAACTCTTCACCAGGGTAGAAGTTGAGTTTATGCCTGTT
TATATCCCAAATGATGTAGAAAAAAAAGACCCCATCCTTTTTGCCAATACAGTACACATCAACATGGCAAATGCTCTAGG
GGTGCCTGGGACAGGGCACACTTATGAAGGCTGCAGAGTGATGATCTCCGCAGGTAACCTTCAACTACCCATAGAAGCTG
GTTTGGTGGAATTTACAAAAATTAGCCAGAAGTTGAAGTTAGATAGGGATAACATTCATCAGCATTTGGATGAATATGCT
GCAATTGCAGTTGCCTCAAAAGGAGGGAAGATAGGAATTGAAGAATTTTCAAGTTATTTAAAACTCCCAATTTCAGAGCC
CTTGAGACAACCCCCTGCCCTCTTCGGCAGGAATAATGATGGCAACATAGACTTCAGAGAGTATGTAATAGGTCTGACTG
TTCTATGCAATCCTGCTAACATTGAAAAGAGTCTGCAAATGTCCTTTAAGCTTTTTGATCTTGATGCGGATGGTTTAATA
ACAGAACAGGAGTTCGCTGCTATACTTCAGGCAGCTTTTGGAGTGCCGGATCTTGATGTTTCCAGGCTCTTTCAGGAAAT
AGCTGGACAGAAATCAGTGTATATTTCATATGAGAGATTTAAGAAATTTGCCCTGAAGCATCCAGCATGTCCCAAGTTAT
TTAATTCACACCTAGACCTCCAGGCAGCCTATATATATTCATTACCCCAAAAAGTACAG

Alignment

ORF - retro_ggor_266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 81.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LILLLAWPFAAISTVCCPEKLT-HPITGWRRKITQTA-LKFLGRAMFFSMGFIVAVKGKIASPLEAPVFV
          ...L..WP.A..ST...P......P...W......T..LK......FF..GF...VKGK.A....AP.FV
Retrocopy IAFLFIWPVAMLSTFGYPAQIL>NPAKSWXXXXGETS>LKLMLQVAFFLPGFLAKVKGKKATQDKAPIFV

Parental  AAPHSTFFDGIACVVAGLPSMVSRNENAQVPLIGRLLRAVQPVLVSRVDPDSRKNTINEIIKRATSGGEW
          .AP.STFFD...CVVAGLPS.VS...N.Q.PL.G..L...Q..LV...DP.SRKNT..EI.K..T.G..W
Retrocopy TAPRSTFFDSFPCVVAGLPSVVSASQNVQIPLAGKVLLSTQLLLVI*EDPHSRKNTKDEILK*VTFGKKW

Parental  PQILVFPEGTCTN-RSCLITFKPGAFIPGVPVQPVLLRYPNKLDTVTWTWQGYTFIQLCMLTFCQLFTKV
          PQIL.F..G.C.N....L..FK.GAF.PGVPV.PVLLRYPN.LD...WTWQG.T..Q.CMLT..QLFT.V
Retrocopy PQILIFL-GVCIN<LARLVIFKLGAFCPGVPV*PVLLRYPNTLDMAIWTWQGFTAFQACMLTLSQLFTRV

Parental  EVEFMPVQVPNDEEKNDPVLFANKVRNLMAEALGIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFTKISR
          EVEFMPV..PND....DP.LFAN.V...MA.ALG.P.T.HTYE.CR.MISAG.L.LP.EAGLVEFTKIS.
Retrocopy EVEFMPVYIPNDVXXXDPILFANTVHINMANALGVPGTGHTYEGCRVMISAGNLQLPIEAGLVEFTKISQ

Parental  KLKLDWDGVRKHLDEYASIASSSKGGRIGIEEFAKYLKLPVSDVLRQLFALFDRNHDGSIDFREYVIGLA
          KLKLD.D....HLDEYA.IA..SKGG.IGIEEF..YLKLP.S..LRQ..ALF.RN.DG.IDFREYVIGL.
Retrocopy KLKLDRDNIHQHLDEYAAIAVASKGGKIGIEEFSSYLKLPISEPLRQPPALFGRNNDGNIDFREYVIGLT

Parental  VLCNPSNTEEIIQVAFKLFDVDEDGYITEEEFSTILQASLGVPDLDVSGLFKEIAQGDS--ISYEEFKSF
          VLCNP.N.E...Q..FKLFD.D.DG.ITE.EF..ILQA..GVPDLDVS.LF.EIA...S..ISYE.FK.F
Retrocopy VLCNPANIEKSLQMSFKLFDLDADGLITEQEFAAILQAAFGVPDLDVSRLFQEIAGQKSVYISYERFKKF

Parental  ALKHPEYAKIFTTYLDLQTCHVFSLPKEVQ
          ALKHP...K.F...LDLQ.....SLP..VQ
Retrocopy ALKHPACPKLFNSHLDLQAAYIYSLPQKVQ

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	0.24 RPM	5.71 RPM
SRP007412_cerebellum	0.00 RPM	2.29 RPM
SRP007412_heart	0.00 RPM	0.88 RPM
SRP007412_kidney	0.00 RPM	5.97 RPM
SRP007412_liver	0.00 RPM	4.64 RPM
SRP007412_testis	0.00 RPM	6.01 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_266 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_185
Pan troglodytes	retro_ptro_171
Macaca mulatta	retro_mmul_392

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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,