RetrogeneDB ID: retro_cjac_2375

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:128091875..128092644(+)
• Located in intron of: ENSCJAG00000003598

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENOPH1
• Ensembl ID: ENSCJAG00000015251
• Aliases: None
• Description: enolase-phosphatase 1 [Source:HGNC Symbol;Acc:24599]

Sequence

>retro_cjac_2375
ATGGTCGTGCTTTCTGTGCCCACCGAAGTCACCGTGATCCCATTAGACATGGAAGGTACCACACCACTGTTGCTTTCTTG
AAGGACATTTTATTCCCTTACCTCAAAGAAAATGTTAAAGAGTATCTGCAGACACAGTGGGAAGAAGAGGCCAGCGGGAG
GTCAGTCTTTGGAGAAAACAGGCTGAAGAGGACGCCCAGCTGGTTGGACTGTTCCTATCTCTGCAGCGTCTGAGAGTGGA
GTGGATGATCCGCAACAGATGATCCAGGCCGTGGTAGATATGTGTGCTGGCAGATGTACCTGGATCGAAAGACCATTGCA
CTCAAACAGCTGCAGGGCCACGTGTGGAGGGCGGCGTTCGCAGCTGGGAGCAGGAAAGCAGAGTTCTTCGCAGATATAGT
TCCAGCTGTCAGGAAGCGGAGAGAGGCTGAAATGAAGATGTATATCTATTCCCTAGCGAGTGTGGAGGCACAGAAACTGT
TGTTTAGGCATTCTATGGAGGAAGATATTCTTGAGCTTGTTGATGGTCACTTTGACACCAAGATTGGACACAAAGTGGAG
AGTGAAAGTTATAGAAAGATTGTAGACAGCATTGGGTGCTCAACCAAAAACATTTTGTTTCTGACAGACGTTACTCAAGA
GGCCAGGGCGGCTGAGGGAGCAGCTGTCATGTAGCTGTAGTGGTGAGCAACACAGGATTAACAGATGATAAGAAGACTTG
CTACAGCCTCATCACATCCTTCAGCGAACTATACCTGCCTCCCTCAACC

Alignment

ORF - retro_cjac_2375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MVVLSVPAEVTVILLDIEGTT-TPIAFVKDILFPYIEKNVKEYLQTHWEEEEC-QQDVSLLRKQAEEDAH
          MVVLSVP.EVTVI.LD.EGTT.T..AF.KDILFPY...NVKEYLQT.WE.EE..Q..VSL.RKQAEEDA.
Retrocopy MVVLSVPTEVTVIPLDMEGTT<TTVAFLKDILFPYLKENVKEYLQTQWE-EEA<QREVSLWRKQAEEDAQ

Parental  LDG-AVPIPAASGSGMDDLQQMIQAVVDN-VCWQMSLDRKTTALKQLQGHMWRTAFTAGLMKAEFFADVV
          L.G..VPI.AAS.SG.DD.QQMIQAVVD..VCWQM.LDRKT.ALKQLQGH.WR.AF.AG..KAEFFAD.V
Retrocopy LVG<TVPISAASESGVDDPQQMIQAVVDM<VCWQMYLDRKTIALKQLQGHVWRAAFAAGSRKAEFFADIV

Parental  PAVRKWREAGMKVYVYSSGSVEAQKLLFGHSTEGDILELVDGHFDTKIGRKVESESYRKIADSIGCSTNN
          PAVRK.REA.MK.Y.YS..SVEAQKLLF.HS.E.DILELVDGHFDTKIG.KVESESYRKI.DSIGCST.N
Retrocopy PAVRKRREAEMKMYIYSLASVEAQKLLFRHSMEEDILELVDGHFDTKIGHKVESESYRKIVDSIGCSTKN

Parental  ILFLTDVTREASAAEEADV-HVAVVVRPGNAGLTDDEKTYYSLITSFSELYLPSST
          ILFLTDVT.EA.AAE.A.V.HVAVVV...N.GLTDD.KT.YSLITSFSELYLP.ST
Retrocopy ILFLTDVTQEARAAEGAAV<HVAVVV--SNTGLTDDKKTCYSLITSFSELYLPPST

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	10.38 RPM
SRP051959_heart	0.00 RPM	13.23 RPM
SRP051959_kidney	0.02 RPM	20.17 RPM
SRP051959_liver	0.00 RPM	9.86 RPM
SRP051959_lung	0.00 RPM	14.38 RPM
SRP051959_lymph_node	0.02 RPM	16.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.25 RPM
SRP051959_spleen	0.04 RPM	17.67 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2375 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2375 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2375 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005140	2 retrocopies	retro_amel_1186, retro_amel_930,
Choloepus hoffmanni	ENSCHOG00000003283	4 retrocopies	retro_chof_2150, retro_chof_470, retro_chof_486, retro_chof_596,
Callithrix jacchus	ENSCJAG00000015251	2 retrocopies	retro_cjac_1376, retro_cjac_2375 ,
Equus caballus	ENSECAG00000019612	1 retrocopy	retro_ecab_164,
Erinaceus europaeus	ENSEEUG00000004274	1 retrocopy	retro_eeur_563,
Homo sapiens	ENSG00000145293	1 retrocopy	retro_hsap_2900,
Gorilla gorilla	ENSGGOG00000003719	1 retrocopy	retro_ggor_2010,
Loxodonta africana	ENSLAFG00000008619	1 retrocopy	retro_lafr_1158,
Macropus eugenii	ENSMEUG00000011458	1 retrocopy	retro_meug_1125,
Myotis lucifugus	ENSMLUG00000014460	1 retrocopy	retro_mluc_2504,
Otolemur garnettii	ENSOGAG00000002502	1 retrocopy	retro_ogar_1549,
Pongo abelii	ENSPPYG00000014887	1 retrocopy	retro_pabe_2399,
Pan troglodytes	ENSPTRG00000016218	1 retrocopy	retro_ptro_1960,
Tursiops truncatus	ENSTTRG00000001800	1 retrocopy	retro_ttru_1231,