RetrogeneDB ID: retro_cjac_3100

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:122987447..122988121(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYPLA1
• Ensembl ID: ENSCJAG00000011562
• Aliases: None
• Description: lysophospholipase I [Source:HGNC Symbol;Acc:6737]

Sequence

>retro_cjac_3100
ATGTGTGACAATGCGAGTCTGCTCTGCTGCTTGCATTGGGGTCCGCTGCCCTGAAGGTCACAGCCATGGTGATTTTTCTT
CATGGATGGGGAGATATCGGGCAAAGATGGGCAGACTTTACAGGTATCAGAAGTTCACATATCAAATATATCTTCCCACA
TGTGCCAGTTATGCCCATGACATTAAATATGAAACATGGCTATGCCTTCTTGGTTTGATGTTATAGGGCCTTTACCAGAT
TCACAGGAGGAGGAACCTGGAATTAAACAGGCAGCAGAAAATGTAAAAGCTTTGGTAGATCAAGAGGTGCAGAATGGCAT
TCTTTCTGGCAGAATTATTTTGGGAGGATTTTCTCAGGGAGGAGCTTTATTTTTATGGACTGCTCTTTTACCACACACAG
TCACTGCACGTGGCTGCTGGATTTCATTTTGGGCTTCCTTTCTAAAGAGTCCTATGAGTGGTGCTGATAGAGATATTTCT
ATTCTCCAGTGCCATGGAGATTGTGACCCATTATTATCCAGATGTTTGGTTTCCTTATATCTTTTTTCTTGTTATGTTGG
TAAATACAGCCAACGTAAACTTTAAAACCTATGCAAGCATAATGCACATTTCATGTCAACAGAAAATGATTGGATGTCAA
GCAATTCACTGATAAAATTCTACCTCCAATTGAT

Alignment

ORF - retro_cjac_3100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MCGNNM-SAQLPAVVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVMPVTLNM-NMA
          MC.N...SA.L.A...AA.K.TA.VIFLHG.GD.G..WA..F.GIRSSHIKYI.PH.PVMP.TLNM.NMA
Retrocopy MCDNAS<SALLLALGSAALKVTAMVIFLHGWGDIGQRWAD-FTGIRSSHIKYIFPHVPVMPMTLNM>NMA

Parental  MPSWFDIIGLSPDSQEDEPGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTMQQKLAG
          MPSWFD.IG..PDSQE.EPGIKQAAEN.KAL.DQEV.NGI.S.RIILGGFSQGGAL.L.TAL......A.
Retrocopy MPSWFDVIGPLPDSQEEEPGIKQAAENVKALVDQEVQNGILSGRIILGGFSQGGALFLWTALLPHTVTAR

Parental  VTALSCWLPLRASFPQGPISGANRDISILQCHGDCDPL-VPLMFGSLT-VEKLKTLVNPANVTFKTYEGM
          ....S.W....ASF...P.SGA.RDISILQCHGDCDPL....MFG.L.....L..LVN.ANV.FKTY...
Retrocopy GCWISFW----ASFLKSPMSGADRDISILQCHGDCDPL<IIQMFGFLI<IFFLVMLVNTANVNFKTYASI

Parental  MHSSCQQEM-MDVKQFIDKVLPPID
          MH.SCQQ.M..DVKQF.DK.LPPID
Retrocopy MHISCQQKM>LDVKQFTDKILPPID

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	0.02 RPM	30.60 RPM
SRP051959_heart	0.00 RPM	22.87 RPM
SRP051959_kidney	0.00 RPM	40.80 RPM
SRP051959_liver	0.00 RPM	37.15 RPM
SRP051959_lung	0.03 RPM	22.21 RPM
SRP051959_lymph_node	0.00 RPM	17.01 RPM
SRP051959_skeletal_muscle	0.00 RPM	23.78 RPM
SRP051959_spleen	0.00 RPM	20.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3100 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3100 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3897
Gorilla gorilla	retro_ggor_2626
Pongo abelii	retro_pabe_3177
Macaca mulatta	retro_mmul_1734

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006978	1 retrocopy	retro_cfam_523,
Callithrix jacchus	ENSCJAG00000011562	2 retrocopies	retro_cjac_1260, retro_cjac_3100 ,
Callithrix jacchus	ENSCJAG00000020914	1 retrocopy	retro_cjac_2585,
Cavia porcellus	ENSCPOG00000022715	3 retrocopies	retro_cpor_142, retro_cpor_549, retro_cpor_782,
Dipodomys ordii	ENSDORG00000001479	1 retrocopy	retro_dord_88,
Equus caballus	ENSECAG00000016530	1 retrocopy	retro_ecab_238,
Echinops telfairi	ENSETEG00000001727	2 retrocopies	retro_etel_612, retro_etel_791,
Homo sapiens	ENSG00000120992	3 retrocopies	retro_hsap_3078, retro_hsap_3485, retro_hsap_3897,
Myotis lucifugus	ENSMLUG00000008208	1 retrocopy	retro_mluc_1683,
Macaca mulatta	ENSMMUG00000013157	3 retrocopies	retro_mmul_1734, retro_mmul_2459, retro_mmul_2474,
Nomascus leucogenys	ENSNLEG00000001027	4 retrocopies	retro_nleu_1137, retro_nleu_2015, retro_nleu_2817, retro_nleu_2869,
Oryctolagus cuniculus	ENSOCUG00000006751	3 retrocopies	retro_ocun_1510, retro_ocun_1623, retro_ocun_1679,
Pongo abelii	ENSPPYG00000018590	3 retrocopies	retro_pabe_2550, retro_pabe_3177, retro_pabe_3565,
Pteropus vampyrus	ENSPVAG00000005246	2 retrocopies	retro_pvam_224, retro_pvam_838,
Rattus norvegicus	ENSRNOG00000008320	3 retrocopies	retro_rnor_1747, retro_rnor_2612, retro_rnor_406,
Tarsius syrichta	ENSTSYG00000012350	6 retrocopies	retro_tsyr_1287, retro_tsyr_1303, retro_tsyr_1465, retro_tsyr_1901, retro_tsyr_1996, retro_tsyr_2158,
Tursiops truncatus	ENSTTRG00000011836	3 retrocopies	retro_ttru_1643, retro_ttru_169, retro_ttru_291,