RetrogeneDB ID: retro_cjac_2945

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:128365497..128366481(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LPCAT2
• Ensembl ID: ENSCJAG00000012902
• Aliases: None
• Description: None

Sequence

>retro_cjac_2945
TCCTGTGTGCTGGCGGGGTTACCCTCAGTGGTCTCTGCAAGTCAAAATGTGCAGATCTCATTGGCTGGGAAATTCCTACT
GTCAACACAGCTGGTGCTTGTGATCCGAGAAGACCCCAATTCCAGGAAGATACTAAGAATGAAATTCTGAAGTGAGTAAC
ATTTGGAAATAAGTGGCCACAGATTCTGATTTTCCTAGAAGGTGTGTGCACCAATCACTGCTGTCTAGTCACTTTTAAAC
TCGGGGCCTTCTGTCCAGGTGTTCCTGTGTAGCCAGTGCTGCTCAGATACCCAAACACCCTGGACATGGCACTCTGGATG
TGGCAGGGATTTACACACTTCCAGGCCTGTATGTTGACCCTCAGGCAACCCTTCACCAAGGTAGAAGTTGCATTTATGCC
TGTTTATATCCCAAATGATGAAGAAAGAAAAGAACCCATCCTTTTTGCTAATAAGTGTGCATCAACATGACAAATGGTCT
GTGGGGTGCCTGTGACAGAGCACACTTACGAAGACTGCAGACTGATGATCCCCGCAGGTAACCTTCAACTACACATAGAA
GCTGGCTTGATGGAATTTACAAAAATTAGCCATAAGTTGAAGTTAGATTGGGGTAACATTAATCAGCATTTGGATGAATA
TGCTGCAATTGCAGTTGCCTCAAAAGGAGGGAAGATAGGAATTGAAGAATTTTTAAGTTATTTAAAACTCCCAATTTCAG
AGCCCTTGAGACAACTTCTTGCCCTCTTTGGCAGGAATAAGGATGGCAGGATAGACTTCAGAGAGTTATGTAATAGTTCT
GACTGTCCTATGCAATCCCGCCAACACTGAAAAGATTCTGCAAATGTCCTTTAAGCTTTTTGATCTTAATGTGGATGGTT
TAATAACAGAACAGGGGTTTGCTGCTATAATTCAGGCAGCTTTTGGAGTGCCAAATCTTGATGTTTCCAGGCTCTTTCAG
TACATAACTGGACAGAAATCAGTG

Alignment

ORF - retro_cjac_2945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.12 %
• Parental protein coverage: 60.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ACIVAGLPSMVSGNSNNQFSSFKGLLRAVQPVLVSRVDPDSRK-NTINEIIKRATSGGEWPQILVFPEGT
          .C..AGLPS.VS...N.Q.S.....L...Q.VLV.R.DP.SRK..T.NEI.K..T.G..WPQIL.F.EG.
Retrocopy SCVLAGLPSVVSASQNVQISLAGKFLLSTQLVLVIREDPNSRK<DTKNEILK*VTFGNKWPQILIFLEGV

Parental  CTNRSCLITFKPGAFIPGVPVQPILLRYPNKLDTVTWTWQGYTFIQLCMLTFCQLFTKVEVEFMPVQVPN
          CTN..CL.TFK.GAF.PGVPV.P.LLRYPN.LD...W.WQG.T..Q.CMLT..Q.FTKVEV.FMPV..PN
Retrocopy CTNHCCLVTFKLGAFCPGVPV*PVLLRYPNTLDMALWMWQGFTHFQACMLTLRQPFTKVEVAFMPVYIPN

Parental  DEEKNDPVLFASRVRNLMAEALGIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFTKISQKLKLDWDGVRR
          DEE...P.LFA...........G.PVT.HTYEDCRLMI.AG.L.L..EAGL.EFTKIS.KLKLDW.....
Retrocopy DEERKEPILFANKCAST*QMVCGVPVTEHTYEDCRLMIPAGNLQLHIEAGLMEFTKISHKLKLDWGNINQ

Parental  HLDEYASIASSSKGGRIGIEEFAEYLKLPVSDVLRQLFALFDRNHDGSIDFRE-YVIGLAVLCHPANTEE
          HLDEYA.IA..SKGG.IGIEEF..YLKLP.S..LRQL.ALF.RN.DG.IDFRE.YVI.L.VLC.PANTE.
Retrocopy HLDEYAAIAVASKGGKIGIEEFLSYLKLPISEPLRQLLALFGRNKDGRIDFRE>YVIVLTVLCNPANTEK

Parental  IIQVAFKLFDVDEDGYITEEEFSTILQASLGVPDLDVSGLFKEIAQGYSI
          I.Q..FKLFD...DG.ITE..F..I.QA..GVP.LDVS.LF..I....S.
Retrocopy ILQMSFKLFDLNVDGLITEQGFAAIIQAAFGVPNLDVSRLFQYITGQKSV

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
SRP051959_colon	0.00 RPM	11.65 RPM
SRP051959_heart	0.00 RPM	2.58 RPM
SRP051959_kidney	0.00 RPM	3.02 RPM
SRP051959_liver	0.00 RPM	5.76 RPM
SRP051959_lung	0.02 RPM	13.91 RPM
SRP051959_lymph_node	0.00 RPM	8.31 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.39 RPM
SRP051959_spleen	0.02 RPM	22.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2945 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2945 has 0 orthologous retrocopies within eutheria group .

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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,