RetrogeneDB ID: retro_cjac_2180

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:123265040..123266180(+)
• Located in intron of: ENSCJAG00000014318

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHAL6A
• Ensembl ID: ENSCJAG00000007067
• Aliases: None
• Description: lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:28335]

Sequence

>retro_cjac_2180
ATGAGCTGGGCTGTGGGAGTCCTGCCCACCAGCGAGAGAATAGGTGCTGCAAAGCTCATTTCCTTCATGGGAGGCTGGCT
CCATGTCCCCACCAGGCTGCATGCATCCTACTTGGGGGTGGCTGGCCCTTCACTCCCATTTCCAAGATGGTGACTGTCAA
GTGTGAACTTGCCAGGAATTTTACTTTGGAGGAGGCCACTCATCCCAATAAGAGCTCCATTATAGGAACTGGATCAGTTG
GCATGGCCTGTGCTCTCAGCATTTTATTAAAAGGTCTGGGCAATGAATTCGCCTTTGTGGATGTCGATTAAAGCAAATTG
AAGGGTGAGACAATGGATCTTCAACATGTCAGCCCTTCCTTAAAAATGCCAAACATGTTTTCCAGCGAAGATTACAGTGT
CACTGCAAAGTCCAGCTTAGTCATTATTGCAGCAGGTGAACGTCCGGCAAAAGGAGAAACGCATCTCCATACAGTCCAGT
GAAATGTGTCCATTTTTAAATTGATGATTTAAAGTACTATCCAGTACAATCCGCACCACAAACTGATAGTGGTTTCTAAT
CCAGTGGCTATTTTAACTTAAATATCCTGTAAATTGAGCGCATTTCCCAAAAACCATGTTATTGAGAGTGGCTGTAATCC
AGACATTGCCTGTTTCCGTTTCTTCATTGGGCAAAGGCTTGATATCCACTCTGAAAGCTGTCATAGGTGGATCCTTGAAG
AGCATGGGGACTTAAGTGCTCCTGTGTGGAATGGAGTGAGTAATGCTGGCGCCCCTCTTGAGGATCTGAACTCAGATAGA
GGAACTCATAAAGATCCTGAACAGTGGAGAAAAGTCCACAAAGAAGTGATTACCTGTGGCTACGAGACAGTTAAAATGAA
AGGTTACACTAATTGGGCCATTAGCCTATTTGTAGCTGATTTAACAGAATGTCCTTTGAAGAATCATAAGAGAGTGTATC
CAGTTTCCACCATAATTAAGGGATTTTATGGAATCAATGAAGTATTCCTCAGCATTCTTCGTATCCTGGGACAGCATGGC
ATTACAGATCTTATGAAGATAAAGCTGTCCCCTGAAGAGGAGACCCAGGTGAAAAAAGAGTGCTGAAAGACTCTGGGAAA
TTTAAAAAGAGCTCAAGCTT

Alignment

ORF - retro_cjac_2180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSWAASVLRSSQRAGAAGADCFCT-RMAPCLRQAVCDLLGSASWRLSCLVSRMATVKGELIKNVAEEKAI
          MSWA..VL..S.R.GAA....F...R.APC..QA.C.LLG...W......S.M.TVK.EL..N...E.A.
Retrocopy MSWAVGVLPTSERIGAAKLISFMG<RLAPCPHQAACILLGGG-WPFTP-ISKMVTVKCELARNFTLEEAT

Parental  HHNKISIVGSGSVGVACAISILLKGLSDELVLVDDDEGKLKGETMDLQHGGPFVKMPKIVSSKDYLVTAN
          H.NK.SI.G.GSVG.ACA.SILLKGL..E...VD.D..KLKGETMDLQH..P..KMP...SS.DY.VTA.
Retrocopy HPNKSSIIGTGSVGMACALSILLKGLGNEFAFVDVD*SKLKGETMDLQHVSPSLKMPNMFSSEDYSVTAK

Parental  SNLVIITAGARQKKGETRLDLVQRNVSIFKLIIPSITQYSPHCKLLIVTNPVDILTYVAWKLSAFPKNRV
          S.LVII.AG.R..KGET.L..VQ.NVSIFKL.I.S..QY.PH.KL..V.NPV.ILT....KLSAFPKN.V
Retrocopy SSLVIIAAGERPAKGETHLHTVQ*NVSIFKLMI*STIQYNPHHKLIVVSNPVAILT*ISCKLSAFPKNHV

Parental  IGSGCNLDSARFRYFIGQRLGIHSESCHGLVLGEHGNSSVPVWSGVNIAGVPLKDLNPDIGTYKDPEQWE
          I.SGCN.D.A.FR.FIGQRL.IHSESCH...L.EHG..S.PVW.GV..AG.PL.DLN.D.GT.KDPEQW.
Retrocopy IESGCNPDIACFRFFIGQRLDIHSESCHRWILEEHGDLSAPVWNGVSNAGAPLEDLNSDRGTHKDPEQWR

Parental  NVHKKVVSSYSGYEMLKMKGYTSWGISLSVADLTESILKNLRRVHPVSTLSKGLYGINEEIFLSVPCILG
          .VHK.V.....GYE..KMKGYT.W.ISL.VADLTE..LKN..RV.PVST..KG.YGIN.E.FLS...ILG
Retrocopy KVHKEVIT--CGYETVKMKGYTNWAISLFVADLTECPLKNHKRVYPVSTIIKGFYGIN-EVFLSILRILG

Parental  ENGIADLIKVKLTLEEEACL-QKSAEILWEIQKELKL
          ..GI.DL.K.KL..EEE.....KSAE.LWEI.KELKL
Retrocopy QHGITDLMKIKLSPEEETQV>KKSAERLWEI*KELKL

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	0.93 RPM	0.95 RPM
SRP051959_heart	0.32 RPM	0.70 RPM
SRP051959_kidney	4.35 RPM	0.58 RPM
SRP051959_liver	0.56 RPM	0.95 RPM
SRP051959_lung	0.31 RPM	1.29 RPM
SRP051959_lymph_node	0.00 RPM	1.07 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.57 RPM
SRP051959_spleen	0.06 RPM	1.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2180 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2180 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007067	2 retrocopies	retro_cjac_164, retro_cjac_2180 ,
Callithrix jacchus	ENSCJAG00000007094	1 retrocopy	retro_cjac_2290,
Homo sapiens	ENSG00000166800	2 retrocopies	retro_hsap_42, retro_hsap_905,
Macaca mulatta	ENSMMUG00000014614	2 retrocopies	retro_mmul_1111, retro_mmul_261,
Nomascus leucogenys	ENSNLEG00000017780	2 retrocopies	retro_nleu_29, retro_nleu_378,
Otolemur garnettii	ENSOGAG00000009261	1 retrocopy	retro_ogar_2662,
Pongo abelii	ENSPPYG00000003435	2 retrocopies	retro_pabe_203, retro_pabe_779,
Pan troglodytes	ENSPTRG00000003423	1 retrocopy	retro_ptro_62,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,