RetrogeneDB ID: retro_cjac_2585

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:493730..494417(-)
• Located in intron of: ENSCJAG00000001308

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYPLA2
• Ensembl ID: ENSCJAG00000020914
• Aliases: None
• Description: lysophospholipase II [Source:HGNC Symbol;Acc:6738]

Sequence

>retro_cjac_2585
ATGTGCGGCAATGACACATTAGCCCAGCTGCCCGCTGTCGTCCCCGCTGCTCCGAGGGCTACTGCCATGGTGATTTTCCT
TCATGGATTGGGAGATACTGGGCACGGATGGGAAGAAGCCTTTGCAGGTATCAGAAATTCACATATCAAATATATCTGCC
CGCATGGGCCTGTTAATGCCTGTTACATTAAATATGAACATGGCTATGCCTTCATGGTTTTATATTATTGGGCTTTCACC
AGATTCACAGGAGGATGAACCTGGGATTAAACAGGCTGCAGAAAACATAAAAGCTTTGATTGATCAAGAAGTGAAGAATG
GCATTACTTCAAAGAGAATTATTTTGGGAGGATTTTCTCAGGGAAGAGCTTTTTATCTTTATATACTGCCCTTACCAGGC
AGCAGAAACTAGCGGGTGTCACTGCACTTAGTTGCTGGCTTCCACTTCGGGCATCATTTCCACAGGGGCCGATCAGTGGC
ACCAATAGAGGTATTTCTATTCTTCAGTGCCACGGAGATTGTGATCCTTTAGTTCCCCTGATGTGTGGTTCTCTTACGGT
TGAAAAACTAAAAACACTGGTGAATTCAGCCAGTGTGACCTTTAAAACCTATGAAGGTATGAGGCACAGTTCGTGTCAAT
AGGCAATGATGGATGTCAAGCAATTCATTGATAAAGTCCTACCTCCA

Alignment

ORF - retro_cjac_2585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.23 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MCGNTMSVPLLTDAATVSGAERETAAVIFLHGLGDTGHSWADALSTIRLPHVKYICPHAP-RIPVTLNMK
          MCGN.....L....A.V..A.R.TA.VIFLHGLGDTGH.W..A...IR..H.KYICPH.P...PVTLNM.
Retrocopy MCGNDTLAQL---PAVVPAAPRATAMVIFLHGLGDTGHGWEEAFAGIRNSHIKYICPHGP>LMPVTLNMN

Parental  MVMPSWFDLMGLSPDAPEDEAGIKKAAENIKALIEHEMKNGIPANRIVPG-RLFGGFSQGGALSLYTALT
          M.MPSWF...GLSPD..EDE.GIK.AAENIKALI..E.KNGI...RI..G.R.F.G.S....LSLYTALT
Retrocopy MAMPSWFYIIGLSPDSQEDEPGIKQAAENIKALIDQEVKNGITSKRIILG<RIFSGKS---FLSLYTALT

Parental  CPHPLAGIVALSCWLPLHRAFPQAA-NGSAKDLAILQCHGELDPMVPVRFGALTAEKLRSVVTPARVQFK
          ....LAG..ALSCWLPL...FPQ....G......ILQCHG..DP.VP...G.LT.EKL...V..A.V.FK
Retrocopy RQQKLAGVTALSCWLPLRASFPQGPISGTNRGISILQCHGDCDPLVPLMCGSLTVEKLKTLVNSASVTFK

Parental  TYPGVMHSSCPQEMAAVKEFLEKLLPP
          TY.G..HSSC...M..VK.F..K.LPP
Retrocopy TYEGMRHSSCQ*AMMDVKQFIDKVLPP

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	0.20 RPM	18.64 RPM
SRP051959_heart	0.30 RPM	6.40 RPM
SRP051959_kidney	0.09 RPM	11.78 RPM
SRP051959_liver	0.06 RPM	10.40 RPM
SRP051959_lung	0.07 RPM	11.94 RPM
SRP051959_lymph_node	0.11 RPM	12.81 RPM
SRP051959_skeletal_muscle	0.13 RPM	8.63 RPM
SRP051959_spleen	0.15 RPM	10.63 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2585 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2585 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2585 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011625	1 retrocopy	retro_btau_1605,
Callithrix jacchus	ENSCJAG00000011562	2 retrocopies	retro_cjac_1260, retro_cjac_3100,
Callithrix jacchus	ENSCJAG00000020914	1 retrocopy	retro_cjac_2585 ,
Dasypus novemcinctus	ENSDNOG00000011285	2 retrocopies	retro_dnov_1186, retro_dnov_134,
Homo sapiens	ENSG00000011009	3 retrocopies	retro_hsap_2023, retro_hsap_3577, retro_hsap_4180,
Gorilla gorilla	ENSGGOG00000004330	3 retrocopies	retro_ggor_2114, retro_ggor_2413, retro_ggor_2626,
Macropus eugenii	ENSMEUG00000004768	2 retrocopies	retro_meug_1134, retro_meug_1526,
Microcebus murinus	ENSMICG00000005841	1 retrocopy	retro_mmur_1166,
Nomascus leucogenys	ENSNLEG00000008646	1 retrocopy	retro_nleu_2958,
Otolemur garnettii	ENSOGAG00000032260	1 retrocopy	retro_ogar_2866,
Pongo abelii	ENSPPYG00000001733	1 retrocopy	retro_pabe_142,
Tursiops truncatus	ENSTTRG00000016127	1 retrocopy	retro_ttru_1522,