RetrogeneDB ID: retro_mmul_392

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:95052738..95054129(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LPCAT2
• Ensembl ID: ENSMMUG00000004478
• Aliases: None
• Description: None

Sequence

>retro_mmul_392
ATGGTCTTACTCTTCCTCTGGCCAGTGGCCATGCTTTCCACCTTTGGCTATCCTGCCCAAATCCTACAACCCTGCCAAGA
GTTGGAAAAAAAAAACTGGTGAAACCAGTACTCAAGCTCATGGTTCAGTTGACTTTCTTTTTAGCAGGGTTCCTAGCTAA
AGTGAAAGGGAAAAAGGCAACCCAAGACAAGGCCCCTATCTTCATTACAGCACCACACTCCACTTTCTTTGACTCAATCC
CCTGTGTGATGGCAGGGTTACCCTCAATGCTCTCTGCAAGTCAAAATGTGCAGATCCCATTGACTGGGAAATTCCTACTG
TCAACACAGCTGGTGCTTGTGATCCGAGAAGACCCCAATTCCAGGAAGAATACTAAGGATGAAATCCTGAAGTGAGTGAC
ATTTGGAAAGAAGTGGCCACAGATTCTGATTTTCCCAGAAGGTGTGTGCATCAATCGCTCCTATCTAGTCACTTTTAAAC
TAGGGGACTTCTGTCCAGGTGTTCCTGTGTAGCCAGTGCTGCTCAGGTACCCAAACACCCTGGACACGGCAGTCTGGACC
TGGCAGGGATTTACAGGCTTCCAGGAATGTATATTGATCCTCAGTCAACACTTCACCAGGGTAGAAGTTGTGTTTATGCC
TGTTTATATCCGAAATGATGAAATAAAAAAAGACCCCATCCTTTTTGCCAATACAATACGCATCAACATGGCAAATGCTC
TGGGGTGCCTGAGACAGAGCACACTTATGAAGACTGCAGACTGATGATCTCCGCAGGTAACCTTCAACTACCCATAGAAG
CTGGTTTGGTGGAATTTACAAAAATTAGCCAGAAGTTGAAGTTAGATAGAGATAACATTCATTAGCATTTGGATGAATAT
GCTGCAATTGCAGTTGCCTCAAAAAGAGGGAAGATAGGAATTGAAGAATTTTCAAGTTATTTAAAACTCCCAATTTCAGA
GCCCTTGAGACAACTTTTTGCCCTCTTTGGCAGGAATAATGCTGGCAGCATAGACTTCAGAGAGTATGTAATAAGTCTGA
CTGTCCTATGCAATCCTGCCAACATTGTAAAGAGTCTGCAAATGTCCTTTAAGCTTTTTGATCTTGATGCGAATGGCTTA
ATAACATAACAGGAGTTCACTGCTATACTTCAGGTAGCTTTTGGAGTGCCAGATCTTGATGTTTCCAGGCTCTTTCAGGA
AATAGCTGGACAGAAATCAGTGTACATTTCATATGAGAAATTTAAGAAATTTGCCCTGAAGCATCAAGCATATTCCAAGT
TATTTAATTCACACCTAGACCTACAGGCAGCCTATATATATTTATTACCCTAAAAAGTACATTTTTAATCACTGTATTCA
AATGTTACAGGTTAGTCCTGAAAATAGTGAA

Alignment

ORF - retro_mmul_392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.46 %
• Parental protein coverage: 84.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LILLLAWPFAAISTVCCPEKLT-HPVTGWRRKITQTA-LKFLGRAMFFSMGFIVSVKGRIASPLEAPVFV
          ..LL..WP.A..ST...P......P...W......T..LK......FF..GF...VKG..A....AP.F.
Retrocopy MVLLFLWPVAMLSTFGYPAQIL>NPAKSWXXXXGETS>LKLMVQLTFFLAGFLAKVKGKKATQDKAPIFI

Parental  AAPHSTFFDGIACVVAGLPSMVSRNENAQVPLIGRMLRAVQPILVSRVDPDSRKNTINEIIKRTTSGGEW
          .APHSTFFD.I.CV.AGLPSM.S...N.Q.PL.G..L...Q..LV.R.DP.SRKNT..EI.K..T.G..W
Retrocopy TAPHSTFFDSIPCVMAGLPSMLSASQNVQIPLTGKFLLSTQLVLVIREDPNSRKNTKDEILK*VTFGKKW

Parental  PQILVFPEGTCTNRSCLITFKPGAFIPGVPVQPVLLRYPNKLDTVTWTWQGYTFIQLCMLTFCQLFTKVE
          PQIL.FPEG.C.NRS.L.TFK.G.F.PGVPV.PVLLRYPN.LDT..WTWQG.T..Q.C.L...Q.FT.VE
Retrocopy PQILIFPEGVCINRSYLVTFKLGDFCPGVPV*PVLLRYPNTLDTAVWTWQGFTGFQECILILSQHFTRVE

Parental  VEFMPVQVPNDEEKNDPVLFANKVRNVMAEAL-GIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFTKISR
          V.FMPV...NDE.K.DP.LFAN..R..MA.AL.G.P.T.HTYEDCRLMISAG.L.LP.EAGLVEFTKIS.
Retrocopy VVFMPVYIRNDEIKKDPILFANTIRINMANAL<GVPETEHTYEDCRLMISAGNLQLPIEAGLVEFTKISQ

Parental  KLKLDWDGVRKQLDEYASIASSSKGGRIGIDEFAKYLKLPVSDVLRQLFALFDRNHDGSIDFREYVIGLA
          KLKLD.D.....LDEYA.IA..SK.G.IGI.EF..YLKLP.S..LRQLFALF.RN..GSIDFREYVI.L.
Retrocopy KLKLDRDNIH*HLDEYAAIAVASKRGKIGIEEFSSYLKLPISEPLRQLFALFGRNNAGSIDFREYVISLT

Parental  VLCNPANTEEIIQVAFKLFDVDEDGYITEEEFSTILQASLGVPDLDVSGLFKEIAQGDS--ISYEEFKSF
          VLCNPAN.....Q..FKLFD.D..G.IT..EF..ILQ...GVPDLDVS.LF.EIA...S..ISYE.FK.F
Retrocopy VLCNPANIVKSLQMSFKLFDLDANGLIT*QEFTAILQVAFGVPDLDVSRLFQEIAGQKSVYISYEKFKKF

Parental  ALRHPEYAKIFTTYLDLQTCHVFSL-PKEVQTTPSIASNKVSPEKHE
          AL.H..Y.K.F...LDLQ......L.PK.......I....VSPE..E
Retrocopy ALKHQAYSKLFNSHLDLQAAYIYLL>PKKYIFNHCIQMLQVSPENSE

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	0.00 RPM	3.47 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	1.43 RPM
SRP007412_cerebellum	0.00 RPM	0.97 RPM
SRP007412_heart	0.00 RPM	0.65 RPM
SRP007412_kidney	0.00 RPM	5.63 RPM
SRP007412_liver	0.00 RPM	2.22 RPM
SRP007412_testis	0.04 RPM	5.84 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_392 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_392 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_185
Pan troglodytes	retro_ptro_171
Gorilla gorilla	retro_ggor_266

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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,