RetrogeneDB ID: retro_ptro_171

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:92835687..92837045(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LPCAT2
• Ensembl ID: ENSPTRG00000008124
• Aliases: LPCAT2, AYTL1
• Description: lysophosphatidylcholine acyltransferase 2 [Source:HGNC Symbol;Acc:26032]

Sequence

>retro_ptro_171
GTACGAATGTCCTGCATTGCCTTCCTCTTCATCTGGCCAGTGGCCATGCTTTCCACCTTTGGCTATCCTGCTCAAATCCT
GCAACCCTGCCAAGAGTTGGAGAAAAAAAACTGGTGAAACCAGTACTCAAGCTCATGCTTCAGGTGGCTTTCTTTTTACC
TGGGTTCCTGGCTAAAGTGAAAGGGAAAAAGGCAACCCAAGACAAGGCCCCTATCTTCGTTACAGCACCACGGTCCACTT
TCTTTGACTCAATCCCCTGTGTGGTGGCAGGGTTACCCTCAGTGGTCTCTGCAAGTCAAAATGTGCAGATCCCATTGGCT
GGGAAATTCCTACTGTCAACACAGCTGGTGCTTGTGATTTGAGAAGACCCCCATTCCAGGAAGAATACTAAGGATGAAAT
CCTGAAGTGAGTGACATTTGGAAAGAAGTGGCCACAGATTCTGATTTTCCTAGAAGGTGTGTGCATCAATCGCTCCCGTC
TAGTCACTTTTAAACTAGGGGCCTTCTGTCCAGGTGTTCCTGTGTAGCCAGTGCTGCTCAGGTACCCAAACACCCTGGAC
ATGGCAATCTGGACCTGGCAGGGATTCACAGCCTTCCAGGCCTGTATGTTGACACTCAGTCAACTCTTCACCAGGGTAGA
AGTTGAGTTTATGCCTGTTTATATCCCAAATGATGAAGAAAAAAAAGACCCCATCCTTTTTGCCAATACAGTACACATCA
ACATGGCAAATGCTCTAGGGGTGCCTGGGACAGGGCACACTTACGAAGGCTGCAGAGTGATGATCTCCGCAGGTAACCTT
CAACTACCCATAGAAGCTGGTTTGGTGGAATTTACAAAAATTAGCCAGAAGTTGAAGTTAGACAGGGATAACATTCATCA
GCATTTGGATGAATATGCTGCAATTGCAGTTGCCTCAAAAGGAGGGAAGATAGGAATTGAAGAATTTTCAAGTTATTTAA
AACTCCCGATTTCAGAGCCCTTGAGACAACCCCCTGCCCACTTCGGCAGGAATAATGATGGCAACATAGACTTCAGAGAG
TATGTAATAGGTCTGACTGTTCTATGCAATCCTGCTAACATTGAAAAGAGTCTGCAAATGTCCTTTAAGCTTTTTGATCT
TGATGCGGATGGTTTAATAACAGAACAGGAGTTCGCTGCTATACTTTAGGCAGCTTTTGGAGTGCCAGATCTTGATGTTT
CCAGGCTCTTTCAGGAAATAGCTGAACAGAAATCAGTGTACATTTCATATGAGAGATTTAAGAAATTTGCCCTGAAGCAT
CCAGCATATCCCAAGTTATTTAATTCACACCTAGACCTCCAGGCAGCCTATATATATTAATTACCCCAAAAAGTACAG

Alignment

ORF - retro_ptro_171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.57 %
• Parental protein coverage: 82.72 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLLVALILLLAWPFAAISTVCCPEKLT-HPITGWRRKITQTA-LKFLGRAMFFSMGFIVAVKGKIASPLE
          V.......L..WP.A..ST...P......P...W......T..LK......FF..GF...VKGK.A....
Retrocopy VRMSCIAFLFIWPVAMLSTFGYPAQIL>NPAKSWXXXXGETS>LKLMLQVAFFLPGFLAKVKGKKATQDK

Parental  APVFVAAPHSTFFDGIACIVAGLPSMVSRNENAQVPLIGRLLRAVQPVLVSRVDPDSRKNTINEIIKRTT
          AP.FV.AP.STFFD.I.C.VAGLPS.VS...N.Q.PL.G..L...Q.VLV...DP.SRKNT..EI.K..T
Retrocopy APIFVTAPRSTFFDSIPCVVAGLPSVVSASQNVQIPLAGKFLLSTQLVLVI*EDPHSRKNTKDEILK*VT

Parental  SGGEWPQILVFPEGTCTNRSCLITFKPGAFIPGVPVQPVLLRYPNKLDTVTWTWQGYTFIQLCMLTFCQL
          .G..WPQIL.F.EG.C.NRS.L.TFK.GAF.PGVPV.PVLLRYPN.LD...WTWQG.T..Q.CMLT..QL
Retrocopy FGKKWPQILIFLEGVCINRSRLVTFKLGAFCPGVPV*PVLLRYPNTLDMAIWTWQGFTAFQACMLTLSQL

Parental  FTKVEVEFMPVQVPNDEEKNDPVLFANKVRNLMAEALGIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFT
          FT.VEVEFMPV..PNDE...DP.LFAN.V...MA.ALG.P.T.HTYE.CR.MISAG.L.LP.EAGLVEFT
Retrocopy FTRVEVEFMPVYIPNDEXXXDPILFANTVHINMANALGVPGTGHTYEGCRVMISAGNLQLPIEAGLVEFT

Parental  KISRKLKLDWDGVRKHLDEYASIASSSKGGRIGIEEFAKYLKLPVSDVLRQLFALFDRNHDGSIDFREYV
          KIS.KLKLD.D....HLDEYA.IA..SKGG.IGIEEF..YLKLP.S..LRQ..A.F.RN.DG.IDFREYV
Retrocopy KISQKLKLDRDNIHQHLDEYAAIAVASKGGKIGIEEFSSYLKLPISEPLRQPPAHFGRNNDGNIDFREYV

Parental  IGLAVLCNPSNTEEIIQVAFKLFDVDEDGYITEEEFSTILQASLGVPDLDVSGLFKEIAQGDS--ISYEE
          IGL.VLCNP.N.E...Q..FKLFD.D.DG.ITE.EF..IL.A..GVPDLDVS.LF.EIA...S..ISYE.
Retrocopy IGLTVLCNPANIEKSLQMSFKLFDLDADGLITEQEFAAIL*AAFGVPDLDVSRLFQEIAEQKSVYISYER

Parental  FKSFALKHPEYAKIFTTYLDLQTCHVFSLPEEVQ
          FK.FALKHP.Y.K.F...LDLQ......LP..VQ
Retrocopy FKKFALKHPAYPKLFNSHLDLQAAYIY*LPQKVQ

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	0.04 RPM	2.93 RPM
SRP007412_cerebellum	0.00 RPM	6.38 RPM
SRP007412_heart	0.00 RPM	1.84 RPM
SRP007412_kidney	0.00 RPM	7.90 RPM
SRP007412_liver	0.00 RPM	4.06 RPM
SRP007412_testis	0.00 RPM	3.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_171 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_171 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_185
Gorilla gorilla	retro_ggor_266
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,